3L71

Cytochrome BC1 complex from chicken with azoxystrobin bound

PDB DOI: https://doi.org/10.2210/pdb3L71/pdb

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.84 Å
R-Value Free: 0.281
R-Value Work: 0.247
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: 480.62 kDa
Atom Count: 32,655
Modelled Residue Count: 4,069
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
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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 Rieske, 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
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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 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download Ideal Coordinates CCD File SDF format, chain SA [auth Q] SDF format, chain WA [auth T] SDF format, chain DA [auth D] SDF format, chain HA [auth G] MOL2 format, chain SA [auth Q] MOL2 format, chain WA [auth T] MOL2 format, chain DA [auth D] MOL2 format, chain HA [auth G]	DA [auth D], HA [auth G], SA [auth Q], WA [auth T]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain DA [auth D] Focus chain HA [auth G] Focus chain SA [auth Q] Focus chain WA [auth T] Interactions & Density Focus chain DA [auth D] Focus chain HA [auth G] Focus chain SA [auth Q] Focus chain WA [auth T]
UQ Query on UQ Download Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain NA [auth P] MOL2 format, chain Z [auth C] MOL2 format, chain NA [auth P]	NA [auth P], Z [auth C]	Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-RECDIHICSA-N		Interactions Focus chain NA [auth P] Focus chain Z [auth C] Interactions & Density Focus chain NA [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 PA [auth P] SDF format, chain IA [auth N] SDF format, chain OA [auth P] SDF format, chain U [auth A] SDF format, chain V [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain PA [auth P] MOL2 format, chain IA [auth N] MOL2 format, chain OA [auth P] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A]	AA [auth C] IA [auth N] OA [auth P] PA [auth P] U [auth A] AA [auth C], IA [auth N], OA [auth P], PA [auth P], U [auth A], V [auth A]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C₄₁ H₇₈ N O₈ P MWRBNPKJOOWZPW-NYVOMTAGSA-N		Interactions Focus chain AA [auth C] Focus chain IA [auth N] Focus chain OA [auth P] Focus chain PA [auth P] Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain AA [auth C] Focus chain IA [auth N] Focus chain OA [auth P] Focus chain PA [auth P] Focus chain U [auth A] Focus chain V [auth A]
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain RA [auth Q] SDF format, chain CA [auth D] MOL2 format, chain RA [auth Q] MOL2 format, chain CA [auth D]	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 JA [auth P] SDF format, chain W [auth C] SDF format, chain KA [auth P] SDF format, chain X [auth C] MOL2 format, chain JA [auth P] MOL2 format, chain W [auth C] MOL2 format, chain KA [auth P] MOL2 format, chain X [auth C]	JA [auth P], KA [auth P], W [auth C], X [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain JA [auth P] Focus chain KA [auth P] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain JA [auth P] Focus chain KA [auth P] Focus chain W [auth C] Focus chain X [auth C]
AZO Query on AZO Download Ideal Coordinates CCD File SDF format, chain MA [auth P] SDF format, chain Y [auth C] MOL2 format, chain MA [auth P] MOL2 format, chain Y [auth C]	MA [auth P], Y [auth C]	METHYL (2Z)-2-(2-{[6-(2-CYANOPHENOXY)PYRIMIDIN-4-YL]OXY}PHENYL)-3-METHOXYACRYLATE C₂₂ H₁₇ N₃ O₅ WFDXOXNFNRHQEC-GHRIWEEISA-N		Interactions Focus chain MA [auth P] Focus chain Y [auth C] Interactions & Density Focus chain MA [auth P] Focus chain Y [auth C]
BOG Query on BOG Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain LA [auth P] SDF format, chain TA [auth Q] SDF format, chain UA [auth Q] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain LA [auth P] MOL2 format, chain TA [auth Q] MOL2 format, chain UA [auth Q]	EA [auth D], FA [auth D], LA [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 LA [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 LA [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]	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 BA [auth C] SDF format, chain QA [auth P] MOL2 format, chain BA [auth C] MOL2 format, chain QA [auth P]	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: 2.84 Å
R-Value Free: 0.281
R-Value Work: 0.247
R-Value Observed: 0.248
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.149	α = 90
b = 181.312	β = 90
c = 240.501	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: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, 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

3L71

Cytochrome BC1 complex from chicken with azoxystrobin 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)