3L75

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 PDBTMMemProtMD

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
R-Value Work: 0.248
R-Value Observed: 0.248

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 480.63 kDa
Atom Count: 32,691
Modelled Residue Count: 4,070
Deposited Residue Count: 4,160
Unique protein chains: 10

Macromolecules

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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
UniProt
Find proteins for D0VX31 (Gallus gallus) Explore D0VX31 Go to UniProtKB: D0VX31
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0VX31
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Reference Sequence

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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
UniProt
Find proteins for D0VX29 (Gallus gallus) Explore D0VX29 Go to UniProtKB: D0VX29
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0VX29
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Reference Sequence

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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
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UniProt Group	P18946
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Reference Sequence

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0VX26
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Reference Sequence

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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 Membrane Entity: Yes
UniProt
Find proteins for Q5ZLR5 (Gallus gallus) Explore Q5ZLR5 Go to UniProtKB: Q5ZLR5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 Membrane Entity: Yes
UniProt
Find proteins for Q5ZLR5 (Gallus gallus) Explore Q5ZLR5 Go to UniProtKB: Q5ZLR5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5ZLR5
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Reference Sequence

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0VX27
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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]	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]	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 BA [auth C] SDF format, chain VA [auth P] SDF format, chain OA [auth N] SDF format, chain U [auth A] SDF format, chain UA [auth P] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain VA [auth P] MOL2 format, chain OA [auth N] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth P]	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 CB [auth Q] SDF format, chain HA [auth D] MOL2 format, chain CB [auth Q] MOL2 format, chain HA [auth D]	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 QA [auth P] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain PA [auth P] MOL2 format, chain QA [auth P] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C]	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 Y [auth C] SDF format, chain SA [auth P] MOL2 format, chain Y [auth C] MOL2 format, chain SA [auth P]	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 FB [auth Q] SDF format, chain EB [auth Q] SDF format, chain GA [auth C] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain RA [auth P] MOL2 format, chain FB [auth Q] MOL2 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]	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 MA [auth E] SDF format, chain GB [auth R] MOL2 format, chain MA [auth E] MOL2 format, chain GB [auth R]	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 CA [auth C] SDF format, chain WA [auth P] MOL2 format, chain CA [auth C] MOL2 format, chain WA [auth P]	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
R-Value Work: 0.248
R-Value Observed: 0.248
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

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

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Help and Resources

3L75

Cytochrome BC1 complex from chicken with fenamidone bound

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

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)