7XMA | pdb_00007xma

Crystal structure of Bovine heart cytochrome c oxidase, apo structure with DMSO

PDB DOI: https://doi.org/10.2210/pdb7XMA/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bos taurus
Mutation(s): No
Membrane Protein: Yes PDBTM mpstruc

Deposited: 2022-04-25 Released: 2022-12-21
Deposition Author(s): Nishida, Y., Shinzawa-Itoh, K., Mizuno, N., Kumasaka, T., Yoshikawa, S., Tsukihara, T., Takashima, S., Shintani, Y.
Funding Organization(s): Japan Science and Technology

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.213 (Depositor), 0.217 (DCC)
R-Value Work:
0.185 (Depositor), 0.191 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases.

Nishida, Y., Yanagisawa, S., Morita, R., Shigematsu, H., Shinzawa-Itoh, K., Yuki, H., Ogasawara, S., Shimuta, K., Iwamoto, T., Nakabayashi, C., Matsumura, W., Kato, H., Gopalasingam, C., Nagao, T., Qaqorh, T., Takahashi, Y., Yamazaki, S., Kamiya, K., Harada, R., Mizuno, N., Takahashi, H., Akeda, Y., Ohnishi, M., Ishii, Y., Kumasaka, T., Murata, T., Muramoto, K., Tosha, T., Shiro, Y., Honma, T., Shigeta, Y., Kubo, M., Takashima, S., Shintani, Y.

(2022) Nat Commun 13: 7591-7591

PubMed: 36481732 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-022-34771-y
Primary Citation Related Structures:
7XMA, 7XMB, 7XMC, 7XMD

PubMed Abstract:
Antimicrobial resistance (AMR) is a global health problem. Despite the enormous efforts made in the last decade, threats from some species, including drug-resistant Neisseria gonorrhoeae, continue to rise and would become untreatable. The development of antibiotics with a different mechanism of action is seriously required. Here, we identified an allosteric inhibitory site buried inside eukaryotic mitochondrial heme-copper oxidases (HCOs), the essential respiratory enzymes for life. The steric conformation around the binding pocket of HCOs is highly conserved among bacteria and eukaryotes, yet the latter has an extra helix. This structural difference in the conserved allostery enabled us to rationally identify bacterial HCO-specific inhibitors: an antibiotic compound against ceftriaxone-resistant Neisseria gonorrhoeae. Molecular dynamics combined with resonance Raman spectroscopy and stopped-flow spectroscopy revealed an allosteric obstruction in the substrate accessing channel as a mechanism of inhibition. Our approach opens fresh avenues in modulating protein functions and broadens our options to overcome AMR.

Organizational Affiliation

Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan.

Macromolecule Content

Total Structure Weight: 521.49 kDa
Atom Count: 33,571
Modeled Residue Count: 3,537
Deposited Residue Count: 4,320
Unique protein chains: 13

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: 7.1.1.9 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,Cytochrome c oxidase subunit 1	B, O	581	Bos taurus	Mutation(s): 0 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for Q6EMS9 (Bos indicus) Explore Q6EMS9 Go to UniProtKB: Q6EMS9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6EMS9
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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	261	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	D, Q	147	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	E, R	109	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
Entity Groups
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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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	85	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	J, W	59	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	K, X	56	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	47	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	M, Z	46	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

Small Molecules

Ligands 14 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download:Ideal Coordinates CCD File SDF format, chain KA [auth C] SDF format, chain OB [auth P] SDF format, chain VA [auth G] SDF format, chain WB [auth T] MOL2 format, chain KA [auth C] MOL2 format, chain OB [auth P] MOL2 format, chain VA [auth G] MOL2 format, chain WB [auth T] mmCIF format, chain KA [auth C] mmCIF format, chain OB [auth P] mmCIF format, chain VA [auth G] mmCIF format, chain WB [auth T]	KA [auth C], OB [auth P], VA [auth G], WB [auth T]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain KA [auth C] Focus chain OB [auth P] Focus chain VA [auth G] Focus chain WB [auth T] Interactions & Density Focus chain KA [auth C] Focus chain OB [auth P] Focus chain VA [auth G] Focus chain WB [auth T]
TGL Query on TGL Download:Ideal Coordinates CCD File SDF format, chain SB [auth Q] SDF format, chain YA [auth L] SDF format, chain YB [auth Y] SDF format, chain QA [auth D] SDF format, chain HB [auth N] SDF format, chain HA [auth A] MOL2 format, chain SB [auth Q] MOL2 format, chain YA [auth L] MOL2 format, chain YB [auth Y] MOL2 format, chain QA [auth D] MOL2 format, chain HB [auth N] MOL2 format, chain HA [auth A] mmCIF format, chain SB [auth Q] mmCIF format, chain YA [auth L] mmCIF format, chain YB [auth Y] mmCIF format, chain QA [auth D] mmCIF format, chain HB [auth N] mmCIF format, chain HA [auth A]	HA [auth A] HB [auth N] QA [auth D] SB [auth Q] YA [auth L] HA [auth A], HB [auth N], QA [auth D], SB [auth Q], YA [auth L], YB [auth Y]	TRISTEAROYLGLYCEROL C₅₇ H₁₁₀ O₆ DCXXMTOCNZCJGO-UHFFFAOYSA-N		Interactions Focus chain HA [auth A] Focus chain HB [auth N] Focus chain QA [auth D] Focus chain SB [auth Q] Focus chain YA [auth L] Focus chain YB [auth Y] Interactions & Density Focus chain HA [auth A] Focus chain HB [auth N] Focus chain QA [auth D] Focus chain SB [auth Q] Focus chain YA [auth L] Focus chain YB [auth Y]
HEA Query on HEA Download:Ideal Coordinates CCD File SDF format, chain AB [auth N] SDF format, chain BA [auth A] SDF format, chain BB [auth N] SDF format, chain AA [auth A] MOL2 format, chain AB [auth N] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth N] MOL2 format, chain AA [auth A] mmCIF format, chain AB [auth N] mmCIF format, chain BA [auth A] mmCIF format, chain BB [auth N] mmCIF format, chain AA [auth A]	AA [auth A], AB [auth N], BA [auth A], BB [auth N]	HEME-A C₄₉ H₅₆ Fe N₄ O₆ ZGGYGTCPXNDTRV-PRYGPKJJSA-L		Interactions Focus chain AA [auth A] Focus chain AB [auth N] Focus chain BA [auth A] Focus chain BB [auth N] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth N] Focus chain BA [auth A] Focus chain BB [auth N]
PEK Query on PEK Download:Ideal Coordinates CCD File SDF format, chain LB [auth P] SDF format, chain OA [auth C] SDF format, chain RB [auth P] SDF format, chain VB [auth T] SDF format, chain UA [auth G] SDF format, chain TA [auth G] MOL2 format, chain LB [auth P] MOL2 format, chain OA [auth C] MOL2 format, chain RB [auth P] MOL2 format, chain VB [auth T] MOL2 format, chain UA [auth G] MOL2 format, chain TA [auth G] mmCIF format, chain LB [auth P] mmCIF format, chain OA [auth C] mmCIF format, chain RB [auth P] mmCIF format, chain VB [auth T] mmCIF format, chain UA [auth G] mmCIF format, chain TA [auth G]	LB [auth P] OA [auth C] RB [auth P] TA [auth G] UA [auth G] LB [auth P], OA [auth C], RB [auth P], TA [auth G], UA [auth G], VB [auth T]	(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 LB [auth P] Focus chain OA [auth C] Focus chain RB [auth P] Focus chain TA [auth G] Focus chain UA [auth G] Focus chain VB [auth T] Interactions & Density Focus chain LB [auth P] Focus chain OA [auth C] Focus chain RB [auth P] Focus chain TA [auth G] Focus chain UA [auth G] Focus chain VB [auth T]
PSC Query on PSC Download:Ideal Coordinates CCD File SDF format, chain KB [auth O] SDF format, chain RA [auth E] MOL2 format, chain KB [auth O] MOL2 format, chain RA [auth E] mmCIF format, chain KB [auth O] mmCIF format, chain RA [auth E]	KB [auth O], RA [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 KB [auth O] Focus chain RA [auth E] Interactions & Density Focus chain KB [auth O] Focus chain RA [auth E]
PGV Query on PGV Download:Ideal Coordinates CCD File SDF format, chain GA [auth A] SDF format, chain IB [auth N] SDF format, chain MB [auth P] SDF format, chain NA [auth C] SDF format, chain NB [auth P] SDF format, chain PA [auth D] SDF format, chain JA [auth C] SDF format, chain GB [auth N] MOL2 format, chain GA [auth A] MOL2 format, chain IB [auth N] MOL2 format, chain MB [auth P] MOL2 format, chain NA [auth C] MOL2 format, chain NB [auth P] MOL2 format, chain PA [auth D] MOL2 format, chain JA [auth C] MOL2 format, chain GB [auth N] mmCIF format, chain GA [auth A] mmCIF format, chain IB [auth N] mmCIF format, chain MB [auth P] mmCIF format, chain NA [auth C] mmCIF format, chain NB [auth P] mmCIF format, chain PA [auth D] mmCIF format, chain JA [auth C] mmCIF format, chain GB [auth N]	GA [auth A] GB [auth N] IB [auth N] JA [auth C] MB [auth P] GA [auth A], GB [auth N], IB [auth N], JA [auth C], MB [auth P], NA [auth C], NB [auth P], PA [auth D]	(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 GA [auth A] Focus chain GB [auth N] Focus chain IB [auth N] Focus chain JA [auth C] Focus chain MB [auth P] Focus chain NA [auth C] Focus chain NB [auth P] Focus chain PA [auth D] Interactions & Density Focus chain GA [auth A] Focus chain GB [auth N] Focus chain IB [auth N] Focus chain JA [auth C] Focus chain MB [auth P] Focus chain NA [auth C] Focus chain NB [auth P] Focus chain PA [auth D]
DMU Query on DMU Download:Ideal Coordinates CCD File SDF format, chain XA [auth J] SDF format, chain XB [auth W] SDF format, chain ZA [auth M] SDF format, chain ZB [auth Z] MOL2 format, chain XA [auth J] MOL2 format, chain XB [auth W] MOL2 format, chain ZA [auth M] MOL2 format, chain ZB [auth Z] mmCIF format, chain XA [auth J] mmCIF format, chain XB [auth W] mmCIF format, chain ZA [auth M] mmCIF format, chain ZB [auth Z]	XA [auth J], XB [auth W], ZA [auth M], ZB [auth Z]	DECYL-BETA-D-MALTOPYRANOSIDE C₂₂ H₄₂ O₁₁ WOQQAWHSKSSAGF-WXFJLFHKSA-N		Interactions Focus chain XA [auth J] Focus chain XB [auth W] Focus chain ZA [auth M] Focus chain ZB [auth Z] Interactions & Density Focus chain XA [auth J] Focus chain XB [auth W] Focus chain ZA [auth M] Focus chain ZB [auth Z]
CHD Query on CHD Download:Ideal Coordinates CCD File SDF format, chain LA [auth C] SDF format, chain PB [auth P] SDF format, chain QB [auth P] SDF format, chain UB [auth T] SDF format, chain WA [auth G] SDF format, chain MA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain PB [auth P] MOL2 format, chain QB [auth P] MOL2 format, chain UB [auth T] MOL2 format, chain WA [auth G] MOL2 format, chain MA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain PB [auth P] mmCIF format, chain QB [auth P] mmCIF format, chain UB [auth T] mmCIF format, chain WA [auth G] mmCIF format, chain MA [auth C]	LA [auth C] MA [auth C] PB [auth P] QB [auth P] UB [auth T] LA [auth C], MA [auth C], PB [auth P], QB [auth P], UB [auth T], WA [auth G]	CHOLIC ACID C₂₄ H₄₀ O₅ BHQCQFFYRZLCQQ-OELDTZBJSA-N		Interactions Focus chain LA [auth C] Focus chain MA [auth C] Focus chain PB [auth P] Focus chain QB [auth P] Focus chain UB [auth T] Focus chain WA [auth G] Interactions & Density Focus chain LA [auth C] Focus chain MA [auth C] Focus chain PB [auth P] Focus chain QB [auth P] Focus chain UB [auth T] Focus chain WA [auth G]
CUA Query on CUA Download:Ideal Coordinates CCD File SDF format, chain IA [auth B] SDF format, chain JB [auth O] MOL2 format, chain IA [auth B] MOL2 format, chain JB [auth O] mmCIF format, chain IA [auth B] mmCIF format, chain JB [auth O]	IA [auth B], JB [auth O]	DINUCLEAR COPPER ION Cu₂ ALKZAGKDWUSJED-UHFFFAOYSA-N		Interactions Focus chain IA [auth B] Focus chain JB [auth O] Interactions & Density Focus chain IA [auth B] Focus chain JB [auth O]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain SA [auth F] SDF format, chain TB [auth S] MOL2 format, chain SA [auth F] MOL2 format, chain TB [auth S] mmCIF format, chain SA [auth F] mmCIF format, chain TB [auth S]	SA [auth F], TB [auth S]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain SA [auth F] Focus chain TB [auth S] Interactions & Density Focus chain SA [auth F] Focus chain TB [auth S]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain CB [auth N] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth N] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth N]	CA [auth A], CB [auth N]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain CB [auth N] Interactions & Density Focus chain CA [auth A] Focus chain CB [auth N]
PER Query on PER Download:Ideal Coordinates CCD File SDF format, chain FA [auth A] SDF format, chain FB [auth N] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth N] mmCIF format, chain FA [auth A] mmCIF format, chain FB [auth N]	FA [auth A], FB [auth N]	PEROXIDE ION O₂ ANAIPYUSIMHBEL-UHFFFAOYSA-N		Interactions Focus chain FA [auth A] Focus chain FB [auth N] Interactions & Density Focus chain FA [auth A] Focus chain FB [auth N]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain DA [auth A] SDF format, chain DB [auth N] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth N] mmCIF format, chain DA [auth A] mmCIF format, chain DB [auth N]	DA [auth A], DB [auth N]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DA [auth A] Focus chain DB [auth N] Interactions & Density Focus chain DA [auth A] Focus chain DB [auth N]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain EA [auth A] SDF format, chain EB [auth N] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth N] mmCIF format, chain EA [auth A] mmCIF format, chain EB [auth N]	EA [auth A], EB [auth N]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain EA [auth A] Focus chain EB [auth N] Interactions & Density Focus chain EA [auth A] Focus chain EB [auth N]

Modified Residues 2 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