6PW1
Cytochrome c Oxidase delta 16
- PDB DOI: https://doi.org/10.2210/pdb6PW1/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Cereibacter sphaeroides 2.4.1
- Expression System: Cereibacter sphaeroides 2.4.1
- Mutation(s): No 
- Membrane Protein: Yes  PDBTMMemProtMD
- Deposited: 2019-07-21 Released: 2019-11-27 
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.204 
- R-Value Work: 0.180 
- R-Value Observed: 0.180 
This is version 2.1 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 c oxidase subunit 1 | 534 | Cereibacter sphaeroides 2.4.1 | Mutation(s): 0  Gene Names: coxI, RSP_1877 EC: 1.9.3.1 Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for Q3J5A7 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3J5A7  Go to UniProtKB:  Q3J5A7 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q3J5A7 | ||||
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 c oxidase subunit 2 | 257 | Cereibacter sphaeroides 2.4.1 | Mutation(s): 0  Gene Names: coxII, RSP_1826 EC: 1.9.3.1 Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for Q3J5G0 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3J5G0  Go to UniProtKB:  Q3J5G0 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q3J5G0 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 9 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
HEA (Subject of Investigation/LOI) Query on HEA | LA [auth C], MA [auth C], U [auth A], V [auth A] | HEME-A C49 H56 Fe N4 O6 ZGGYGTCPXNDTRV-PRYGPKJJSA-L | |||
DMU Query on DMU | BA [auth B] KA [auth C] Q [auth A] R [auth A] S [auth A] | DECYL-BETA-D-MALTOPYRANOSIDE C22 H42 O11 WOQQAWHSKSSAGF-WXFJLFHKSA-N | |||
TRD Query on TRD | AA [auth B] G [auth A] H [auth A] I [auth A] IA [auth C] | TRIDECANE C13 H28 IIYFAKIEWZDVMP-UHFFFAOYSA-N | |||
HTH Query on HTH | HA [auth B], Z [auth A] | (2S,3R)-heptane-1,2,3-triol C7 H16 O3 HXYCHJFUBNTKQR-RQJHMYQMSA-N | |||
TRS Query on TRS | CA [auth B] | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O | |||
CD Query on CD | FA [auth B], GA [auth B], TA [auth D], UA [auth D] | CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N | |||
CU Query on CU | DA [auth B] EA [auth B] NA [auth C] RA [auth D] SA [auth D] | COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N | |||
CA Query on CA | PA [auth C], Y [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
MG Query on MG | OA [auth C], X [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900001 Query on PRD_900001 | E, F | alpha-maltose | Oligosaccharide / Nutrient |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.204 
- R-Value Work: 0.180 
- R-Value Observed: 0.180 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 123.315 | α = 90 |
b = 130 | β = 90 |
c = 177.539 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
HKL-2000 | data scaling |
PHASER | phasing |
HKL-2000 | data reduction |
Entry History & Funding Information
Deposition Data
- Released Date: 2019-11-27  Deposition Author(s): Liu, J., Ferguson-Miller, S.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | -- |
Revision History (Full details and data files)
- Version 1.0: 2019-11-27
Type: Initial release - Version 1.1: 2019-12-11
Changes: Database references - Version 1.2: 2020-01-01
Changes: Author supporting evidence - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2023-10-11
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary