5IY5 | pdb_00005iy5

Electron transfer complex of cytochrome c and cytochrome c oxidase at 2.0 angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb5IY5/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bos taurus, Equus caballus
Mutation(s): Yes
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2016-03-24 Released: 2017-01-11
Deposition Author(s): Shimada, S., Baba, J., Aoe, S., Shimada, A., Yamashita, E., Tsukihara, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.207 (Depositor)
R-Value Work:
0.167 (Depositor)
R-Value Observed:
0.169 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Complex structure of cytochrome c-cytochrome c oxidase reveals a novel protein-protein interaction mode

Shimada, S., Shinzawa-Itoh, K., Baba, J., Aoe, S., Shimada, A., Yamashita, E., Kang, J., Tateno, M., Yoshikawa, S., Tsukihara, T.

(2017) EMBO J 36: 291-300

PubMed: 27979921 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.15252/embj.201695021
Primary Citation Related Structures:
5IY5

PubMed Abstract:
Mitochondrial cytochrome c oxidase (CcO) transfers electrons from cytochrome c (Cyt.c) to O ₂ to generate H ₂O, a process coupled to proton pumping. To elucidate the mechanism of electron transfer, we determined the structure of the mammalian Cyt.c-CcO complex at 2.0-Å resolution and identified an electron transfer pathway from Cyt.c to CcO. The specific interaction between Cyt.c and CcO is stabilized by a few electrostatic interactions between side chains within a small contact surface area. Between the two proteins are three water layers with a long inter-molecular span, one of which lies between the other two layers without significant direct interaction with either protein. Cyt.c undergoes large structural fluctuations, using the interacting regions with CcO as a fulcrum. These features of the protein-protein interaction at the docking interface represent the first known example of a new class of protein-protein interaction, which we term "soft and specific". This interaction is likely to contribute to the rapid association/dissociation of the Cyt.c-CcO complex, which facilitates the sequential supply of four electrons for the O ₂ reduction reaction.

Organizational Affiliation

Picobiology Institute, Graduate School of Life Science, University of Hyogo, Akoh, Hyogo, Japan.

Macromolecule Content

Total Structure Weight: 456.56 kDa
Atom Count: 34,765
Modeled Residue Count: 3,768
Deposited Residue Count: 3,768
Unique protein chains: 14

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	A, N	514	Bos taurus	Mutation(s): 0 EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P00396 (Bos taurus) Explore P00396 Go to UniProtKB: P00396
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00396
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Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 2	B, O	227	Bos taurus	Mutation(s): 0 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for P68530 (Bos taurus) Explore P68530 Go to UniProtKB: P68530
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68530
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 3	C, P	259	Bos taurus	Mutation(s): 0 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for P00415 (Bos taurus) Explore P00415 Go to UniProtKB: P00415
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00415
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial	D, Q	144	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00423 (Bos taurus) Explore P00423 Go to UniProtKB: P00423
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00423
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 5A, mitochondrial	E, R	105	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00426 (Bos taurus) Explore P00426 Go to UniProtKB: P00426
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00426
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Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 5B, mitochondrial	F, S	98	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00428 (Bos taurus) Explore P00428 Go to UniProtKB: P00428
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00428
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Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6A2, mitochondrial	G, T	84	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07471 (Bos taurus) Explore P07471 Go to UniProtKB: P07471
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07471
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6B1	H, U	79	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00429 (Bos taurus) Explore P00429 Go to UniProtKB: P00429
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00429
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6C	I, V	73	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P04038 (Bos taurus) Explore P04038 Go to UniProtKB: P04038
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04038
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7A1, mitochondrial	J, W	58	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07470 (Bos taurus) Explore P07470 Go to UniProtKB: P07470
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07470
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7B, mitochondrial	K, X	49	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P13183 (Bos taurus) Explore P13183 Go to UniProtKB: P13183
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13183
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Reference Sequence

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| 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7C, mitochondrial	L, Y	46	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00430 (Bos taurus) Explore P00430 Go to UniProtKB: P00430
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00430
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Reference Sequence

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| 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 8B, mitochondrial	M, Z	43	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P10175 (Bos taurus) Explore P10175 Go to UniProtKB: P10175
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10175
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Reference Sequence

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| 3D Structure

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c	AA [auth 1], BA [auth 2]	105	Equus caballus	Mutation(s): 1
UniProt
Find proteins for P00004 (Equus caballus) Explore P00004 Go to UniProtKB: P00004
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00004
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Reference Sequence

Small Molecules

Ligands 17 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download:Ideal Coordinates CCD File SDF format, chain DB [auth G] SDF format, chain GC [auth P] SDF format, chain OC [auth T] SDF format, chain SA [auth C] MOL2 format, chain DB [auth G] MOL2 format, chain GC [auth P] MOL2 format, chain OC [auth T] MOL2 format, chain SA [auth C] mmCIF format, chain DB [auth G] mmCIF format, chain GC [auth P] mmCIF format, chain OC [auth T] mmCIF format, chain SA [auth C]	DB [auth G], GC [auth P], OC [auth T], SA [auth C]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain DB [auth G] Focus chain GC [auth P] Focus chain OC [auth T] Focus chain SA [auth C] Interactions & Density Focus chain DB [auth G] Focus chain GC [auth P] Focus chain OC [auth T] Focus chain SA [auth C]
TGL Query on TGL Download:Ideal Coordinates CCD File SDF format, chain JB [auth L] SDF format, chain KA [auth B] SDF format, chain LC [auth Q] SDF format, chain YA [auth D] SDF format, chain TB [auth N] MOL2 format, chain JB [auth L] MOL2 format, chain KA [auth B] MOL2 format, chain LC [auth Q] MOL2 format, chain YA [auth D] MOL2 format, chain TB [auth N] mmCIF format, chain JB [auth L] mmCIF format, chain KA [auth B] mmCIF format, chain LC [auth Q] mmCIF format, chain YA [auth D] mmCIF format, chain TB [auth N]	JB [auth L], KA [auth B], LC [auth Q], TB [auth N], YA [auth D]	TRISTEAROYLGLYCEROL C₅₇ H₁₁₀ O₆ DCXXMTOCNZCJGO-UHFFFAOYSA-N		Interactions Focus chain JB [auth L] Focus chain KA [auth B] Focus chain LC [auth Q] Focus chain TB [auth N] Focus chain YA [auth D] Interactions & Density Focus chain JB [auth L] Focus chain KA [auth B] Focus chain LC [auth Q] Focus chain TB [auth N] Focus chain YA [auth D]
HEA Query on HEA Download:Ideal Coordinates CCD File SDF format, chain GA [auth A] SDF format, chain QB [auth N] SDF format, chain RB [auth N] SDF format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain QB [auth N] MOL2 format, chain RB [auth N] MOL2 format, chain FA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain QB [auth N] mmCIF format, chain RB [auth N] mmCIF format, chain FA [auth A]	FA [auth A], GA [auth A], QB [auth N], RB [auth N]	HEME-A C₄₉ H₅₆ Fe N₄ O₆ ZGGYGTCPXNDTRV-PRYGPKJJSA-L		Interactions Focus chain FA [auth A] Focus chain GA [auth A] Focus chain QB [auth N] Focus chain RB [auth N] Interactions & Density Focus chain FA [auth A] Focus chain GA [auth A] Focus chain QB [auth N] Focus chain RB [auth N]
PEK Query on PEK Download:Ideal Coordinates CCD File SDF format, chain DC [auth P] SDF format, chain PA [auth C] MOL2 format, chain DC [auth P] MOL2 format, chain PA [auth C] mmCIF format, chain DC [auth P] mmCIF format, chain PA [auth C]	DC [auth P], PA [auth C]	(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE C₄₃ H₇₈ N O₈ P ANRKEHNWXKCXDB-BHFWLYLHSA-N		Interactions Focus chain DC [auth P] Focus chain PA [auth C] Interactions & Density Focus chain DC [auth P] Focus chain PA [auth C]
PSC Query on PSC Download:Ideal Coordinates CCD File SDF format, chain RC [auth V] SDF format, chain ZA [auth E] MOL2 format, chain RC [auth V] MOL2 format, chain ZA [auth E] mmCIF format, chain RC [auth V] mmCIF format, chain ZA [auth E]	RC [auth V], ZA [auth E]	(7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE C₄₂ H₈₁ N O₈ P JLPULHDHAOZNQI-AUSZDXHESA-O		Interactions Focus chain RC [auth V] Focus chain ZA [auth E] Interactions & Density Focus chain RC [auth V] Focus chain ZA [auth E]
PGV Query on PGV Download:Ideal Coordinates CCD File SDF format, chain EC [auth P] SDF format, chain FC [auth P] SDF format, chain IA [auth A] SDF format, chain JA [auth A] SDF format, chain RA [auth C] SDF format, chain XB [auth N] SDF format, chain QA [auth C] MOL2 format, chain EC [auth P] MOL2 format, chain FC [auth P] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain XB [auth N] MOL2 format, chain QA [auth C] mmCIF format, chain EC [auth P] mmCIF format, chain FC [auth P] mmCIF format, chain IA [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain XB [auth N] mmCIF format, chain QA [auth C]	EC [auth P] FC [auth P] IA [auth A] JA [auth A] QA [auth C] EC [auth P], FC [auth P], IA [auth A], JA [auth A], QA [auth C], RA [auth C], XB [auth N]	(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE C₄₀ H₇₇ O₁₀ P ADYWCMPUNIVOEA-GPJPVTGXSA-N		Interactions Focus chain EC [auth P] Focus chain FC [auth P] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain XB [auth N] Interactions & Density Focus chain EC [auth P] Focus chain FC [auth P] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain XB [auth N]
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain WC [auth 1] SDF format, chain XC [auth 2] MOL2 format, chain WC [auth 1] MOL2 format, chain XC [auth 2] mmCIF format, chain WC [auth 1] mmCIF format, chain XC [auth 2]	WC [auth 1], XC [auth 2]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain WC [auth 1] Focus chain XC [auth 2] Interactions & Density Focus chain WC [auth 1] Focus chain XC [auth 2]
DMU Query on DMU Download:Ideal Coordinates CCD File SDF format, chain LB [auth M] SDF format, chain VC [auth Z] MOL2 format, chain LB [auth M] MOL2 format, chain VC [auth Z] mmCIF format, chain LB [auth M] mmCIF format, chain VC [auth Z]	LB [auth M], VC [auth Z]	DECYL-BETA-D-MALTOPYRANOSIDE C₂₂ H₄₂ O₁₁ WOQQAWHSKSSAGF-WXFJLFHKSA-N		Interactions Focus chain LB [auth M] Focus chain VC [auth Z] Interactions & Density Focus chain LB [auth M] Focus chain VC [auth Z]
CHD Query on CHD Download:Ideal Coordinates CCD File SDF format, chain BC [auth P] SDF format, chain EB [auth G] SDF format, chain HB [auth J] SDF format, chain HC [auth P] SDF format, chain NA [auth C] SDF format, chain QC [auth T] SDF format, chain SC [auth W] SDF format, chain TA [auth C] MOL2 format, chain BC [auth P] MOL2 format, chain EB [auth G] MOL2 format, chain HB [auth J] MOL2 format, chain HC [auth P] MOL2 format, chain NA [auth C] MOL2 format, chain QC [auth T] MOL2 format, chain SC [auth W] MOL2 format, chain TA [auth C] mmCIF format, chain BC [auth P] mmCIF format, chain EB [auth G] mmCIF format, chain HB [auth J] mmCIF format, chain HC [auth P] mmCIF format, chain NA [auth C] mmCIF format, chain QC [auth T] mmCIF format, chain SC [auth W] mmCIF format, chain TA [auth C]	BC [auth P] EB [auth G] HB [auth J] HC [auth P] NA [auth C] BC [auth P], EB [auth G], HB [auth J], HC [auth P], NA [auth C], QC [auth T], SC [auth W], TA [auth C]	CHOLIC ACID C₂₄ H₄₀ O₅ BHQCQFFYRZLCQQ-OELDTZBJSA-N		Interactions Focus chain BC [auth P] Focus chain EB [auth G] Focus chain HB [auth J] Focus chain HC [auth P] Focus chain NA [auth C] Focus chain QC [auth T] Focus chain SC [auth W] Focus chain TA [auth C] Interactions & Density Focus chain BC [auth P] Focus chain EB [auth G] Focus chain HB [auth J] Focus chain HC [auth P] Focus chain NA [auth C] Focus chain QC [auth T] Focus chain SC [auth W] Focus chain TA [auth C]
CUA Query on CUA Download:Ideal Coordinates CCD File SDF format, chain AC [auth O] SDF format, chain LA [auth B] MOL2 format, chain AC [auth O] MOL2 format, chain LA [auth B] mmCIF format, chain AC [auth O] mmCIF format, chain LA [auth B]	AC [auth O], LA [auth B]	DINUCLEAR COPPER ION Cu₂ ALKZAGKDWUSJED-UHFFFAOYSA-N		Interactions Focus chain AC [auth O] Focus chain LA [auth B] Interactions & Density Focus chain AC [auth O] Focus chain LA [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain BB [auth F] SDF format, chain MC [auth S] MOL2 format, chain BB [auth F] MOL2 format, chain MC [auth S] mmCIF format, chain BB [auth F] mmCIF format, chain MC [auth S]	BB [auth F], MC [auth S]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BB [auth F] Focus chain MC [auth S] Interactions & Density Focus chain BB [auth F] Focus chain MC [auth S]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain NB [auth N] MOL2 format, chain CA [auth A] MOL2 format, chain NB [auth N] mmCIF format, chain CA [auth A] mmCIF format, chain NB [auth N]	CA [auth A], NB [auth N]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain NB [auth N] Interactions & Density Focus chain CA [auth A] Focus chain NB [auth N]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AB [auth E] SDF format, chain CB [auth F] SDF format, chain FB [auth G] SDF format, chain GB [auth I] SDF format, chain MA [auth B] SDF format, chain NC [auth S] SDF format, chain YB [auth N] SDF format, chain ZB [auth N] SDF format, chain XA [auth C] MOL2 format, chain AB [auth E] MOL2 format, chain CB [auth F] MOL2 format, chain FB [auth G] MOL2 format, chain GB [auth I] MOL2 format, chain MA [auth B] MOL2 format, chain NC [auth S] MOL2 format, chain YB [auth N] MOL2 format, chain ZB [auth N] MOL2 format, chain XA [auth C] mmCIF format, chain AB [auth E] mmCIF format, chain CB [auth F] mmCIF format, chain FB [auth G] mmCIF format, chain GB [auth I] mmCIF format, chain MA [auth B] mmCIF format, chain NC [auth S] mmCIF format, chain YB [auth N] mmCIF format, chain ZB [auth N] mmCIF format, chain XA [auth C]	AB [auth E] CB [auth F] FB [auth G] GB [auth I] MA [auth B] AB [auth E], CB [auth F], FB [auth G], GB [auth I], MA [auth B], NC [auth S], XA [auth C], YB [auth N], ZB [auth N]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth E] Focus chain CB [auth F] Focus chain FB [auth G] Focus chain GB [auth I] Focus chain MA [auth B] Focus chain NC [auth S] Focus chain XA [auth C] Focus chain YB [auth N] Focus chain ZB [auth N] Interactions & Density Focus chain AB [auth E] Focus chain CB [auth F] Focus chain FB [auth G] Focus chain GB [auth I] Focus chain MA [auth B] Focus chain NC [auth S] Focus chain XA [auth C] Focus chain YB [auth N] Focus chain ZB [auth N]
PER Query on PER Download:Ideal Coordinates CCD File SDF format, chain HA [auth A] SDF format, chain SB [auth N] MOL2 format, chain HA [auth A] MOL2 format, chain SB [auth N] mmCIF format, chain HA [auth A] mmCIF format, chain SB [auth N]	HA [auth A], SB [auth N]	PEROXIDE ION O₂ ANAIPYUSIMHBEL-UHFFFAOYSA-N		Interactions Focus chain HA [auth A] Focus chain SB [auth N] Interactions & Density Focus chain HA [auth A] Focus chain SB [auth N]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain DA [auth A] SDF format, chain OB [auth N] MOL2 format, chain DA [auth A] MOL2 format, chain OB [auth N] mmCIF format, chain DA [auth A] mmCIF format, chain OB [auth N]	DA [auth A], OB [auth N]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DA [auth A] Focus chain OB [auth N] Interactions & Density Focus chain DA [auth A] Focus chain OB [auth N]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain CC [auth P] SDF format, chain OA [auth C] SDF format, chain PB [auth N] SDF format, chain EA [auth A] MOL2 format, chain CC [auth P] MOL2 format, chain OA [auth C] MOL2 format, chain PB [auth N] MOL2 format, chain EA [auth A] mmCIF format, chain CC [auth P] mmCIF format, chain OA [auth C] mmCIF format, chain PB [auth N] mmCIF format, chain EA [auth A]	CC [auth P], EA [auth A], OA [auth C], PB [auth N]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain CC [auth P] Focus chain EA [auth A] Focus chain OA [auth C] Focus chain PB [auth N] Interactions & Density Focus chain CC [auth P] Focus chain EA [auth A] Focus chain OA [auth C] Focus chain PB [auth N]
UNL Query on UNL Download:Ideal Coordinates CCD File	IB [auth J] IC [auth P] JC [auth P] KB [auth L] KC [auth P] IB [auth J], IC [auth P], JC [auth P], KB [auth L], KC [auth P], MB [auth N], PC [auth T], TC [auth W], UA [auth C], UB [auth N], UC [auth Y], VA [auth C], VB [auth N], WA [auth C], WB [auth N]	Unknown ligand FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain IB [auth J] Focus chain IC [auth P] Focus chain JC [auth P] Focus chain KB [auth L] Focus chain KC [auth P] Focus chain MB [auth N] Focus chain PC [auth T] Focus chain TC [auth W] Focus chain UA [auth C] Focus chain UB [auth N] Focus chain UC [auth Y] Focus chain VA [auth C] Focus chain VB [auth N] Focus chain WA [auth C] Focus chain WB [auth N] Interactions & Density Focus chain IB [auth J] Focus chain IC [auth P] Focus chain JC [auth P] Focus chain KB [auth L] Focus chain KC [auth P] Focus chain MB [auth N] Focus chain PC [auth T] Focus chain TC [auth W] Focus chain UA [auth C] Focus chain UB [auth N] Focus chain UC [auth Y] Focus chain VA [auth C] Focus chain VB [auth N] Focus chain WA [auth C] Focus chain WB [auth N]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME Query on FME	A, N	L-PEPTIDE LINKING	C₆ H₁₁ N O₃ S		MET
TPO Query on TPO	G, T	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR
SAC Query on SAC	I, V	L-PEPTIDE LINKING	C₅ H₉ N O₄		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.207 (Depositor)
R-Value Work: 0.167 (Depositor)
R-Value Observed: 0.169 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.29	α = 90
b = 183.872	β = 102.12
c = 148.929	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-01-11

Deposition Author(s):

Funding Organization	Location	Grant Number
	Japan	--

Revision History (Full details and data files)

Version 1.0: 2017-01-11
Type: Initial release
Version 1.1: 2017-02-15
Changes: Database references
Version 2.0: 2019-10-09
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

5IY5 | pdb_00005iy5

Electron transfer complex of cytochrome c and cytochrome c oxidase at 2.0 angstrom resolution

Literature

Complex structure of cytochrome c-cytochrome c oxidase reveals a novel protein-protein interaction mode

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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UniProt

Entity Groups

Sequence Annotations

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Entity ID: 6

UniProt

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Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

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Sequence Annotations

Entity ID: 10

UniProt

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Entity ID: 11

UniProt

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Entity ID: 12

UniProt

Entity Groups

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Entity ID: 13

UniProt

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Entity ID: 14

UniProt

Entity Groups

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)