Research workbench
Catalytic core subunits (I and II) of cytochrome C oxidase from rhodobacter sphaeroides in the reduced state
Analyse Catalytic core subunits (I and II) of cytochrome C oxidase from rhodobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FYE
- Type
- protein
- Length
- 1,578 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C oxidase subunit 1; Cytochrome C oxidase subunit 2
- EC
- 1.9.3.1
- UniProt
- P33517, Q03736
- Ligands
- TRD, HEA, HTO, CU1, CD, MG, CA, UNX
- Pockets
- 16 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 65% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C oxidase subunit 1 (EC 1.9.3.1) | protein | 535 | 72% helix, 2% strand | P33517 |
| B, D | Cytochrome C oxidase subunit 2 (EC 1.9.3.1) | protein | 256 | 37% helix, 25% strand | Q03736 |
| C | Cytochrome C oxidase subunit 1 (EC 1.9.3.1) | protein | 531 | 71% helix, 2% strand | P33517 |
Ligands and binding sites
- TRD · Tridecane · ligand · 12 copies · chains A, B, C, D
- HEA · Heme-A · ligand · 4 copies · chains A, B, C, D
- HTO · Heptane-1,2,3-triol · ligand · chains B
- CU1 · Copper (I) ion · metal · 6 copies · chains A, B, C, D
- CD · Cadmium ion · metal · 4 copies · chains B, D
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, C
- UNX · Unknown atom or ion · ion · 2 copies · chains A, C
- DMU · Decyl-beta-D-maltopyranoside · additive · 10 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1100 | 0.90 | 0.92 | 113 | HEA |
| 2 | 1124 | 0.90 | 0.92 | 120 | HEA, DMU |
| 3 | 322 | 0.69 | 0.82 | 29 | empty |
| 4 | 332 | 0.66 | 0.80 | 29 | empty |
| 5 | 128 | 0.51 | 0.80 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–B · 4036 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 3982 Ų buried · 52 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3FYE · Catalytic core subunits (I and II) of cytochrome c oxidase from Rhodobacter sphaeroides… · the same entry in another collection · chain D against D, TM-score 1.00
- P33517 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit 1 (P33517) · a predicted model of the same protein · chain A against A, TM-score 1.00
- Q03736 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit 2 (Q03736) · a predicted model of the same protein · chain B against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P33517
- Every structure of UniProt Q03736
- Elsewhere: RCSB PDB 3FYE · PDBe 3FYE · UniProt P33517 · UniProt Q03736
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