3CWB
Chicken Cytochrome BC1 Complex inhibited by an iodinated analogue of the polyketide Crocacin-D
- PDB DOI: https://doi.org/10.2210/pdb3CWB/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Gallus gallus
- Mutation(s): No
- Membrane Protein: Yes OPMPDBTMMemProtMD
- Deposited: 2008-04-21 Released: 2008-08-12
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.51 Å
- R-Value Free: 0.319
- R-Value Work: 0.285
- R-Value Observed: 0.285
This is version 2.0 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 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 |  |
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 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 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 |  |
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 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome b | C, M [auth P] | 380 | Gallus gallus | Mutation(s): 0 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 | ||||
Sequence AnnotationsExpand | |||||
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(by identity cutoff) | 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 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR PROTEIN | E, O [auth R] | 196 | Gallus gallus | Mutation(s): 0 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 | ||||
Sequence AnnotationsExpand | |||||
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(by identity cutoff) | 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 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 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 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 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 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
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 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 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 9 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, leader sequence | I, S [auth V] | 52 | Gallus gallus | Mutation(s): 0 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 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 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 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 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 10 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CDL Query on CDL | FA [auth D], JA [auth G], QA [auth P], RA [auth P] | CARDIOLIPIN C81 H156 O17 P2 XVTUQDWPJJBEHJ-KZCWQMDCSA-L |  | ||
| UQ Query on UQ | AA [auth C], PA [auth P] | Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer C59 H90 O4 ACTIUHUUMQJHFO-RECDIHICSA-N |  | ||
| PEE Query on PEE | BA [auth C] BB [auth W] CA [auth C] SA [auth P] TA [auth P] | 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C41 H78 N O8 P MWRBNPKJOOWZPW-NYVOMTAGSA-N |  | ||
| HEC Query on HEC | EA [auth D], YA [auth Q] | HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N |  | ||
| HEM Query on HEM | MA [auth P], NA [auth P], X [auth C], Y [auth C] | PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L |  | ||
| ICX Query on ICX | OA [auth P], Z [auth C] | methyl N-[(5Z)-6-({[4-(4-iodobenzyl)phenyl]carbonyl}amino)hex-5-enoyl]glycinate C23 H25 I N2 O4 GJXNVOLPXGNHOU-CPSFFCFKSA-N |  | ||
| BOG Query on BOG | DA [auth D] GA [auth E] KA [auth P] V [auth C] WA [auth Q] | octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N |  | ||
| FES Query on FES | AB [auth R], HA [auth E] | FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N |  | ||
| AZI Query on AZI | LA [auth P], W [auth C] | AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N |  | ||
| UNL Query on UNL | IA [auth E], UA [auth P], VA [auth P], ZA [auth Q] | Unknown ligand IVRMZWNICZWHMI-UHFFFAOYSA-N | |||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.51 Å
- R-Value Free: 0.319
- R-Value Work: 0.285
- R-Value Observed: 0.285
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 174.778 | α = 90 |
| b = 182.663 | β = 90 |
| c = 242.945 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| Blu-Ice | data collection |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| CNS | phasing |
Entry History
Deposition Data
- Released Date: 2008-08-12 Deposition Author(s): Huang, L., Cromartie, T., Viner, R., Crowley, P.J., Berry, E.A.
Revision History (Full details and data files)
- Version 1.0: 2008-08-12
Type: Initial release - Version 1.1: 2011-07-13
Changes: Derived calculations, Version format compliance - Version 1.2: 2014-10-29
Changes: Non-polymer description - Version 1.3: 2017-10-25
Changes: Advisory, Refinement description - Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 2.0: 2023-08-30
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary
