3L75 | pdb_00003l75

Cytochrome BC1 complex from chicken with fenamidone bound

PDB DOI: https://doi.org/10.2210/pdb3L75/pdb

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

Deposited: 2009-12-28 Released: 2010-02-02
Deposition Author(s): Huang, L., Berry, E.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free:
0.275 (Depositor), 0.267 (DCC)
R-Value Work:
0.248 (Depositor), 0.236 (DCC)
R-Value Observed:
0.248 (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: 480.63 kDa
Atom Count: 32,691
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
Sequence Annotations Expand
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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| 3D Structure

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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| 3D Structure

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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| 3D Structure

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
Sequence Annotations Expand
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 10 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 Q] SDF format, chain IA [auth D] SDF format, chain IB [auth T] SDF format, chain NA [auth G] MOL2 format, chain DB [auth Q] MOL2 format, chain IA [auth D] MOL2 format, chain IB [auth T] MOL2 format, chain NA [auth G] mmCIF format, chain DB [auth Q] mmCIF format, chain IA [auth D] mmCIF format, chain IB [auth T] mmCIF format, chain NA [auth G]	DB [auth Q], IA [auth D], IB [auth T], NA [auth G]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain DB [auth Q] Focus chain IA [auth D] Focus chain IB [auth T] Focus chain NA [auth G] Interactions & Density Focus chain DB [auth Q] Focus chain IA [auth D] Focus chain IB [auth T] Focus chain NA [auth G]
UQ Query on UQ Download:Ideal Coordinates CCD File SDF format, chain TA [auth P] SDF format, chain Z [auth C] MOL2 format, chain TA [auth P] MOL2 format, chain Z [auth C] mmCIF format, chain TA [auth P] mmCIF format, chain Z [auth C]	TA [auth P], Z [auth C]	Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-RECDIHICSA-N		Interactions Focus chain TA [auth P] Focus chain Z [auth C] Interactions & Density Focus chain TA [auth P] Focus chain Z [auth C]
PEE Query on PEE Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain OA [auth N] SDF format, chain U [auth A] SDF format, chain UA [auth P] SDF format, chain VA [auth P] SDF format, chain BA [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain OA [auth N] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth P] MOL2 format, chain VA [auth P] MOL2 format, chain BA [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain OA [auth N] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth P] mmCIF format, chain VA [auth P] mmCIF format, chain BA [auth C]	AA [auth C] BA [auth C] OA [auth N] U [auth A] UA [auth P] AA [auth C], BA [auth C], OA [auth N], U [auth A], UA [auth P], VA [auth P]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C₄₁ H₇₈ N O₈ P MWRBNPKJOOWZPW-NYVOMTAGSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain OA [auth N] Focus chain U [auth A] Focus chain UA [auth P] Focus chain VA [auth P] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain OA [auth N] Focus chain U [auth A] Focus chain UA [auth P] Focus chain VA [auth P]
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain HA [auth D] SDF format, chain CB [auth Q] MOL2 format, chain HA [auth D] MOL2 format, chain CB [auth Q] mmCIF format, chain HA [auth D] mmCIF format, chain CB [auth Q]	CB [auth Q], HA [auth D]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain CB [auth Q] Focus chain HA [auth D] Interactions & Density Focus chain CB [auth Q] Focus chain HA [auth D]
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain PA [auth P] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain QA [auth P] MOL2 format, chain PA [auth P] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain QA [auth P] mmCIF format, chain PA [auth P] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain QA [auth P]	PA [auth P], QA [auth P], W [auth C], X [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain PA [auth P] Focus chain QA [auth P] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain PA [auth P] Focus chain QA [auth P] Focus chain W [auth C] Focus chain X [auth C]
FNM Query on FNM Download:Ideal Coordinates CCD File SDF format, chain SA [auth P] SDF format, chain Y [auth C] MOL2 format, chain SA [auth P] MOL2 format, chain Y [auth C] mmCIF format, chain SA [auth P] mmCIF format, chain Y [auth C]	SA [auth P], Y [auth C]	(5S)-5-methyl-2-(methylsulfanyl)-5-phenyl-3-(phenylamino)-3,5-dihydro-4H-imidazol-4-one C₁₇ H₁₇ N₃ O S LMVPQMGRYSRMIW-KRWDZBQOSA-N		Interactions Focus chain SA [auth P] Focus chain Y [auth C] Interactions & Density Focus chain SA [auth P] Focus chain Y [auth C]
BOG Query on BOG Download:Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain RA [auth P] SDF format, chain FB [auth Q] SDF format, chain EB [auth Q] MOL2 format, chain GA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain RA [auth P] MOL2 format, chain FB [auth Q] MOL2 format, chain EB [auth Q] mmCIF format, chain GA [auth C] mmCIF format, chain JA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain RA [auth P] mmCIF format, chain FB [auth Q] mmCIF format, chain EB [auth Q]	EB [auth Q] FB [auth Q] GA [auth C] JA [auth D] KA [auth D] EB [auth Q], FB [auth Q], GA [auth C], JA [auth D], KA [auth D], RA [auth P]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain EB [auth Q] Focus chain FB [auth Q] Focus chain GA [auth C] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain RA [auth P] Interactions & Density Focus chain EB [auth Q] Focus chain FB [auth Q] Focus chain GA [auth C] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain RA [auth P]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain GB [auth R] SDF format, chain MA [auth E] MOL2 format, chain GB [auth R] MOL2 format, chain MA [auth E] mmCIF format, chain GB [auth R] mmCIF format, chain MA [auth E]	GB [auth R], MA [auth E]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain GB [auth R] Focus chain MA [auth E] Interactions & Density Focus chain GB [auth R] Focus chain MA [auth E]
AZI Query on AZI Download:Ideal Coordinates CCD File SDF format, chain WA [auth P] SDF format, chain CA [auth C] MOL2 format, chain WA [auth P] MOL2 format, chain CA [auth C] mmCIF format, chain WA [auth P] mmCIF format, chain CA [auth C]	CA [auth C], WA [auth P]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain WA [auth P] Interactions & Density Focus chain CA [auth C] Focus chain WA [auth P]
UNL Query on UNL Download:Ideal Coordinates CCD File	AB [auth P] BB [auth P] DA [auth C] EA [auth C] FA [auth C] AB [auth P], BB [auth P], DA [auth C], EA [auth C], FA [auth C], HB [auth R], LA [auth D], V [auth A], XA [auth P], YA [auth P], ZA [auth P]	Unknown ligand IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain AB [auth P] Focus chain BB [auth P] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain HB [auth R] Focus chain LA [auth D] Focus chain V [auth A] Focus chain XA [auth P] Focus chain YA [auth P] Focus chain ZA [auth P] Interactions & Density Focus chain AB [auth P] Focus chain BB [auth P] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain HB [auth R] Focus chain LA [auth D] Focus chain V [auth A] Focus chain XA [auth P] Focus chain YA [auth P] Focus chain ZA [auth P]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free: 0.275 (Depositor), 0.267 (DCC)
R-Value Work: 0.248 (Depositor), 0.236 (DCC)
R-Value Observed: 0.248 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 172.285	α = 90
b = 182.141	β = 90
c = 241.198	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	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.

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: 2017-11-01
Changes: Refinement description
Version 1.4: 2018-02-14
Changes: Experimental preparation
Version 1.5: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, 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

3L75 | pdb_00003l75

Cytochrome BC1 complex from chicken with fenamidone 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)