2QJP
Crystal structure of wild type rhodobacter sphaeroides with stigmatellin and antimycin inhibited
- PDB DOI: https://doi.org/10.2210/pdb2QJP/pdb
- Classification: ELECTRON TRANSPORT
- Organism(s): Cereibacter sphaeroides
- Expression System: Escherichia coli
- Mutation(s): No 
- Membrane Protein: Yes  OPMPDBTMMemProtMD
- Deposited: 2007-07-08 Released: 2007-12-25 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.277 
- R-Value Work: 0.244 
- R-Value Observed: 0.244 
This is version 1.3 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 |
Cytochrome b | 428 | Cereibacter sphaeroides | Mutation(s): 0  Gene Names: petB, fbcB Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for Q02761 (Cereibacter sphaeroides) Explore Q02761  Go to UniProtKB:  Q02761 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q02761 | ||||
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 |
Cytochrome c1 | 256 | Cereibacter sphaeroides | Mutation(s): 0  Gene Names: fbcC Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for Q02760 (Cereibacter sphaeroides) Explore Q02760  Go to UniProtKB:  Q02760 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q02760 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Ubiquinol-cytochrome c reductase iron-sulfur subunit | 179 | Cereibacter sphaeroides | Mutation(s): 0  Gene Names: petA, fbcF EC: 1.10.2.2 Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for Q02762 (Cereibacter sphaeroides) Explore Q02762  Go to UniProtKB:  Q02762 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q02762 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 7 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
LOP Query on LOP | JA [auth G], Q [auth A], TA [auth J], Y [auth D] | (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE C35 H68 N O8 P FUUNMZKPCMPCHT-ILGKRYBBSA-N | |||
HEM Query on HEM | CA [auth E] GA [auth G] HA [auth G] MA [auth H] N [auth A] | PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L | |||
ANJ Query on ANJ | KA [auth G], R [auth A], UA [auth J], Z [auth D] | (2R,3S,6S,7R,8R)-3-{[3-(FORMYLAMINO)-2-HYDROXYBENZOYL]AMINO}-8-HEXYL-2,6-DIMETHYL-4,9-DIOXO-1,5-DIOXONAN-7-YL (2S)-2-METHYLBUTANOATE C28 H40 N2 O9 UPHOMQADKXDOFD-UKHQZXFMSA-N | |||
SMA Query on SMA | IA [auth G], P [auth A], SA [auth J], X [auth D] | STIGMATELLIN A C30 H42 O7 UZHDGDDPOPDJGM-WPPYOTIYSA-N | |||
BGL Query on BGL | AA [auth E], EA [auth G], M [auth A], OA [auth J] | 2-O-octyl-beta-D-glucopyranose C14 H28 O6 BVHPDIWLWHHJPD-RKQHYHRCSA-N | |||
FES Query on FES | DA [auth F], NA [auth I], U [auth C], XA [auth L] | FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N | |||
SR Query on SR | BA [auth E] FA [auth G] LA [auth H] PA [auth J] S [auth B] | STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.277 
- R-Value Work: 0.244 
- R-Value Observed: 0.244 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 135.061 | α = 90 |
b = 146.52 | β = 110.21 |
c = 141.003 | γ = 90 |
Software Name | Purpose |
---|---|
CNS | refinement |
HKL-2000 | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | phasing |
Entry History 
Revision History (Full details and data files)
- Version 1.0: 2007-12-25
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.3: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary