3L72 | pdb_00003l72

Chicken cytochrome BC1 complex with kresoxim-I-dimethyl bound

PDB DOI: https://doi.org/10.2210/pdb3L72/pdb

Classification: OXIDOREDUCTASE
Organism(s): Gallus gallus
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2009-12-27 Released: 2010-02-02
Deposition Author(s): Huang, L., Zhang, Z., Berry, E.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.06 Å
R-Value Free:
0.294 (Depositor), 0.281 (DCC)
R-Value Work:
0.264 (Depositor), 0.252 (DCC)
R-Value Observed:
0.264 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Famoxadone and related inhibitors bind like methoxy acrylate inhibitors in the Qo site of the BC1 compl and fix the rieske iron-sulfur protein in a positio close to but distinct from that seen with stigmatellin and other "DISTAL" Qo inhibitors.

Huang, L., Berry, E.A.

To be published.

Macromolecule Content

Total Structure Weight: 480.72 kDa
Atom Count: 32,648
Modeled Residue Count: 4,070
Deposited Residue Count: 4,160
Unique protein chains: 10

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN I	A, K [auth N]	446	Gallus gallus	Mutation(s): 0 EC: 1.10.2.2 Membrane Entity: Yes
UniProt
Find proteins for D0VX31 (Gallus gallus) Explore D0VX31 Go to UniProtKB: D0VX31
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VX31
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2	B, L [auth O]	441	Gallus gallus	Mutation(s): 0 EC: 1.10.2.2 Membrane Entity: Yes
UniProt
Find proteins for D0VX29 (Gallus gallus) Explore D0VX29 Go to UniProtKB: D0VX29
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VX29
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME B	C, M [auth P]	380	Gallus gallus	Mutation(s): 0 EC: 1.10.2.2 Membrane Entity: Yes
UniProt
Find proteins for P18946 (Gallus gallus) Explore P18946 Go to UniProtKB: P18946
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P18946
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
MITOCHONDRIAL CYTOCHROME C1, HEME PROTEIN	D, N [auth Q]	241	Gallus gallus	Mutation(s): 0 EC: 1.10.2.2 Membrane Entity: Yes
UniProt
Find proteins for D0VX26 (Gallus gallus) Explore D0VX26 Go to UniProtKB: D0VX26
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VX26
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME B-C1 COMPLEX SUBUNIT 5, RIESKE IRONSULFUR PROTEIN, MITOCHONDRIAL	E, O [auth R]	196	Gallus gallus	Mutation(s): 0 EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for Q5ZLR5 (Gallus gallus) Explore Q5ZLR5 Go to UniProtKB: Q5ZLR5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5ZLR5
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 14 KDA PROTEIN	F, P [auth S]	110	Gallus gallus	Mutation(s): 0 EC: 1.10.2.2 Membrane Entity: Yes
UniProt
Find proteins for D0VX30 (Gallus gallus) Explore D0VX30 Go to UniProtKB: D0VX30
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VX30
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE UBIQUINONE-BINDING PROTEIN QP-C	G, Q [auth T]	81	Gallus gallus	Mutation(s): 0 EC: 1.10.2.2 Membrane Entity: Yes
UniProt
Find proteins for D0VX32 (Gallus gallus) Explore D0VX32 Go to UniProtKB: D0VX32
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VX32
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 11 KDA PROTEIN, COMPLEX III SUBUNIT VIII	H, R [auth U]	77	Gallus gallus	Mutation(s): 0 EC: 1.10.2.2 Membrane Entity: Yes
UniProt
Find proteins for D0VX28 (Gallus gallus) Explore D0VX28 Go to UniProtKB: D0VX28
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VX28
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL	I, S [auth V]	47	Gallus gallus	Mutation(s): 0 EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for Q5ZLR5 (Gallus gallus) Explore Q5ZLR5 Go to UniProtKB: Q5ZLR5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5ZLR5
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Reference Sequence

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| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 7.2 KDA PROTEIN	J, T [auth W]	61	Gallus gallus	Mutation(s): 0 EC: 1.10.2.2 Membrane Entity: Yes
UniProt
Find proteins for D0VX27 (Gallus gallus) Explore D0VX27 Go to UniProtKB: D0VX27
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VX27
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain SA [auth Q] SDF format, chain NA [auth P] SDF format, chain DA [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain SA [auth Q] MOL2 format, chain NA [auth P] MOL2 format, chain DA [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain SA [auth Q] mmCIF format, chain NA [auth P] mmCIF format, chain DA [auth D]	DA [auth D], NA [auth P], SA [auth Q], Y [auth C]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain DA [auth D] Focus chain NA [auth P] Focus chain SA [auth Q] Focus chain Y [auth C] Interactions & Density Focus chain DA [auth D] Focus chain NA [auth P] Focus chain SA [auth Q] Focus chain Y [auth C]
UQ Query on UQ Download:Ideal Coordinates CCD File SDF format, chain MA [auth P] SDF format, chain X [auth C] MOL2 format, chain MA [auth P] MOL2 format, chain X [auth C] mmCIF format, chain MA [auth P] mmCIF format, chain X [auth C]	MA [auth P], X [auth C]	Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-RECDIHICSA-N		Interactions Focus chain MA [auth P] Focus chain X [auth C] Interactions & Density Focus chain MA [auth P] Focus chain X [auth C]
PEE Query on PEE Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain WA [auth R] SDF format, chain PA [auth P] SDF format, chain OA [auth P] SDF format, chain HA [auth E] SDF format, chain AA [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain WA [auth R] MOL2 format, chain PA [auth P] MOL2 format, chain OA [auth P] MOL2 format, chain HA [auth E] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain WA [auth R] mmCIF format, chain PA [auth P] mmCIF format, chain OA [auth P] mmCIF format, chain HA [auth E] mmCIF format, chain AA [auth C]	AA [auth C] HA [auth E] OA [auth P] PA [auth P] WA [auth R] AA [auth C], HA [auth E], OA [auth P], PA [auth P], WA [auth R], Z [auth C]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C₄₁ H₇₈ N O₈ P MWRBNPKJOOWZPW-NYVOMTAGSA-N		Interactions Focus chain AA [auth C] Focus chain HA [auth E] Focus chain OA [auth P] Focus chain PA [auth P] Focus chain WA [auth R] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain HA [auth E] Focus chain OA [auth P] Focus chain PA [auth P] Focus chain WA [auth R] Focus chain Z [auth C]
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain RA [auth Q] MOL2 format, chain CA [auth D] MOL2 format, chain RA [auth Q] mmCIF format, chain CA [auth D] mmCIF format, chain RA [auth Q]	CA [auth D], RA [auth Q]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain CA [auth D] Focus chain RA [auth Q] Interactions & Density Focus chain CA [auth D] Focus chain RA [auth Q]
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain IA [auth P] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain JA [auth P] MOL2 format, chain IA [auth P] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain JA [auth P] mmCIF format, chain IA [auth P] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain JA [auth P]	IA [auth P], JA [auth P], U [auth C], V [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain IA [auth P] Focus chain JA [auth P] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain IA [auth P] Focus chain JA [auth P] Focus chain U [auth C] Focus chain V [auth C]
IKR Query on IKR Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain LA [auth P] MOL2 format, chain W [auth C] MOL2 format, chain LA [auth P] mmCIF format, chain W [auth C] mmCIF format, chain LA [auth P]	LA [auth P], W [auth C]	methyl (2E)-{2-[(4-iodo-2,5-dimethylphenoxy)methyl]phenyl}(methoxyimino)ethanoate C₁₉ H₂₀ I N O₄ QNSHGJNFUSNVMK-DYTRJAOYSA-N		Interactions Focus chain LA [auth P] Focus chain W [auth C] Interactions & Density Focus chain LA [auth P] Focus chain W [auth C]
BOG Query on BOG Download:Ideal Coordinates CCD File SDF format, chain UA [auth Q] SDF format, chain TA [auth Q] SDF format, chain KA [auth P] SDF format, chain FA [auth D] SDF format, chain EA [auth D] MOL2 format, chain UA [auth Q] MOL2 format, chain TA [auth Q] MOL2 format, chain KA [auth P] MOL2 format, chain FA [auth D] MOL2 format, chain EA [auth D] mmCIF format, chain UA [auth Q] mmCIF format, chain TA [auth Q] mmCIF format, chain KA [auth P] mmCIF format, chain FA [auth D] mmCIF format, chain EA [auth D]	EA [auth D], FA [auth D], KA [auth P], TA [auth Q], UA [auth Q]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain EA [auth D] Focus chain FA [auth D] Focus chain KA [auth P] Focus chain TA [auth Q] Focus chain UA [auth Q] Interactions & Density Focus chain EA [auth D] Focus chain FA [auth D] Focus chain KA [auth P] Focus chain TA [auth Q] Focus chain UA [auth Q]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain VA [auth R] SDF format, chain GA [auth E] MOL2 format, chain VA [auth R] MOL2 format, chain GA [auth E] mmCIF format, chain VA [auth R] mmCIF format, chain GA [auth E]	GA [auth E], VA [auth R]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain GA [auth E] Focus chain VA [auth R] Interactions & Density Focus chain GA [auth E] Focus chain VA [auth R]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain QA [auth P] SDF format, chain BA [auth C] MOL2 format, chain QA [auth P] MOL2 format, chain BA [auth C] mmCIF format, chain QA [auth P] mmCIF format, chain BA [auth C]	BA [auth C], QA [auth P]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain QA [auth P] Interactions & Density Focus chain BA [auth C] Focus chain QA [auth P]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.06 Å
R-Value Free: 0.294 (Depositor), 0.281 (DCC)
R-Value Work: 0.264 (Depositor), 0.252 (DCC)
R-Value Observed: 0.264 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 172.614	α = 90
b = 181.548	β = 90
c = 241.033	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-02-02

Deposition Author(s):

Huang, L.

Zhang, Z.

Berry, E.A.

Revision History (Full details and data files)

Version 1.0: 2010-02-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2014-10-29
Changes: Non-polymer description
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2021-05-05
Changes: Structure summary
Version 2.0: 2023-09-06
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, 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.

3L72 | pdb_00003l72

Chicken cytochrome BC1 complex with kresoxim-I-dimethyl bound

Literature

Famoxadone and related inhibitors bind like methoxy acrylate inhibitors in the Qo site of the BC1 compl and fix the rieske iron-sulfur protein in a positio close to but distinct from that seen with stigmatellin and other "DISTAL" Qo inhibitors.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)