3H1H

Cytochrome bc1 complex from chicken

PDB DOI: https://doi.org/10.2210/pdb3H1H/pdb

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

Deposited: 2009-04-12 Released: 2009-04-28
Deposition Author(s): Zhang, Z., Huang, L., Shulmeister, V.M., Chi, Y.I., Kim, K.K., Hung, L.W., Crofts, A.R., Berry, E.A., Kim, S.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.16 Å
R-Value Free: 0.291
R-Value Work: 0.253
R-Value Observed: 0.253

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 479.84 kDa
Atom Count: 32,608
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
UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN I, MITOCHONDRIAL	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
UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2, MITOCHONDRIAL	B, L [auth O]	441	Gallus gallus	Mutation(s): 0 EC: 1.10.2.2
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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
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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
CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL	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
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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
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UniProt Group	Q5ZLR5
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KDA PROTEIN	F, P [auth S]	110	Gallus gallus	Mutation(s): 0 EC: 1.10.2.2
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 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
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UniProt Group	D0VX32
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 11 KDA PROTEIN	H, R [auth U]	77	Gallus gallus	Mutation(s): 0 EC: 1.10.2.2
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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
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UniProt Group	Q5ZLR5
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 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
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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 AA [auth C] SDF format, chain HA [auth D] SDF format, chain VA [auth P] SDF format, chain ZA [auth Q] MOL2 format, chain AA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain VA [auth P] MOL2 format, chain ZA [auth Q]	AA [auth C], HA [auth D], VA [auth P], ZA [auth Q]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain AA [auth C] Focus chain HA [auth D] Focus chain VA [auth P] Focus chain ZA [auth Q] Interactions & Density Focus chain AA [auth C] Focus chain HA [auth D] Focus chain VA [auth P] Focus chain ZA [auth Q]
UQ Query on UQ Download Ideal Coordinates CCD File SDF format, chain UA [auth P] SDF format, chain Z [auth C] MOL2 format, chain UA [auth P] MOL2 format, chain Z [auth C]	UA [auth P], Z [auth C]	Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-RECDIHICSA-N		Interactions Focus chain UA [auth P] Focus chain Z [auth C] Interactions & Density Focus chain UA [auth P] Focus chain Z [auth C]
PEE Query on PEE Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DB [auth R] SDF format, chain OA [auth N] SDF format, chain WA [auth P] SDF format, chain LA [auth E] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DB [auth R] MOL2 format, chain OA [auth N] MOL2 format, chain WA [auth P] MOL2 format, chain LA [auth E]	BA [auth C] CA [auth C] DB [auth R] LA [auth E] OA [auth N] BA [auth C], CA [auth C], DB [auth R], LA [auth E], OA [auth N], WA [auth P]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C₄₁ H₇₈ N O₈ P MWRBNPKJOOWZPW-NYVOMTAGSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DB [auth R] Focus chain LA [auth E] Focus chain OA [auth N] Focus chain WA [auth P] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DB [auth R] Focus chain LA [auth E] Focus chain OA [auth N] Focus chain WA [auth P]
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain YA [auth Q] MOL2 format, chain GA [auth D] MOL2 format, chain YA [auth Q]	GA [auth D], YA [auth Q]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain GA [auth D] Focus chain YA [auth Q] Interactions & Density Focus chain GA [auth D] Focus chain YA [auth Q]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain RA [auth P] SDF format, chain X [auth C] SDF format, chain QA [auth P] SDF format, chain Y [auth C] MOL2 format, chain RA [auth P] MOL2 format, chain X [auth C] MOL2 format, chain QA [auth P] MOL2 format, chain Y [auth C]	QA [auth P], RA [auth P], X [auth C], Y [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain QA [auth P] Focus chain RA [auth P] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain QA [auth P] Focus chain RA [auth P] Focus chain X [auth C] Focus chain Y [auth C]
BOG Query on BOG Download Ideal Coordinates CCD File SDF format, chain AB [auth Q] SDF format, chain BB [auth Q] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain SA [auth P] MOL2 format, chain AB [auth Q] MOL2 format, chain BB [auth Q] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain SA [auth P]	AB [auth Q], BB [auth Q], IA [auth D], JA [auth D], SA [auth P]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain AB [auth Q] Focus chain BB [auth Q] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain SA [auth P] Interactions & Density Focus chain AB [auth Q] Focus chain BB [auth Q] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain SA [auth P]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain CB [auth R] SDF format, chain KA [auth E] MOL2 format, chain CB [auth R] MOL2 format, chain KA [auth E]	CB [auth R], KA [auth E]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain CB [auth R] Focus chain KA [auth E] Interactions & Density Focus chain CB [auth R] Focus chain KA [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain XA [auth P] MOL2 format, chain DA [auth C] MOL2 format, chain XA [auth P]	DA [auth C], XA [auth P]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain XA [auth P] Interactions & Density Focus chain DA [auth C] Focus chain XA [auth P]
UNL Query on UNL Download Ideal Coordinates CCD File	EA [auth C] FA [auth C] MA [auth N] NA [auth N] PA [auth N] EA [auth C], FA [auth C], MA [auth N], NA [auth N], PA [auth N], TA [auth P], U [auth A], V [auth A], W [auth A]	Unknown ligand PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain FA [auth C] Focus chain MA [auth N] Focus chain NA [auth N] Focus chain PA [auth N] Focus chain TA [auth P] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Interactions & Density Focus chain EA [auth C] Focus chain FA [auth C] Focus chain MA [auth N] Focus chain NA [auth N] Focus chain PA [auth N] Focus chain TA [auth P] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.16 Å
R-Value Free: 0.291
R-Value Work: 0.253
R-Value Observed: 0.253
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.59	α = 90
b = 182.518	β = 90
c = 240.573	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
RAVE	model building
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
RAVE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-04-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-04-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary

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Help and Resources

3H1H

Cytochrome bc1 complex from chicken

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

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

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

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)