Research workbench
Catalytic core subunits (I and II) of cytochrome C oxidase from rhodobacter sphaeroides with E101A (II) mutation
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
- 6CI0
- Type
- protein
- Length
- 1,579 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, HTH, GLC, CU, MG, CA, CD, K
- Pockets
- 13 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 10% 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 | Cytochrome C oxidase subunit 2 (EC 1.9.3.1) | protein | 256 | 38% helix, 26% strand | Q03736 |
| C | Cytochrome C oxidase subunit 1 (EC 1.9.3.1) | protein | 531 | 71% helix, 2% strand | P33517 |
| D | Cytochrome C oxidase subunit 2 (EC 1.9.3.1) | protein | 257 | 37% helix, 25% strand | Q03736 |
Ligands and binding sites
- TRD · Tridecane · ligand · 14 copies · chains A, B, C, D
- HEA · Heme-A · ligand · 4 copies · chains A, B, C, D
- HTH · (2S,3R)-heptane-1,2,3-triol · ligand · 3 copies · chains B, A
- GLC · alpha-D-glucopyranose · sugar · 6 copies · chains B, D, C
- CU · Copper (II) ion · metal · 6 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, C
- CD · Cadmium ion · metal · 2 copies · chains B, D
- K · Potassium ion · metal
- DMU · Decyl-beta-D-maltopyranoside · additive · 6 copies · chains A, B, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.90 | 0.91 | 115 | HEA |
| 2 | 1170 | 0.89 | 0.91 | 130 | DMU, HEA |
| 3 | 332 | 0.68 | 0.81 | 31 | TRD |
| 4 | 327 | 0.66 | 0.81 | 27 | empty |
| 5 | 118 | 0.50 | 0.80 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3966 Ų buried · 52 hydrogen bonds · protein-protein
- C–D · 3963 Ų buried · 48 hydrogen bonds · protein-protein
- B–D · 158 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 54 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6CI0 · 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 6CI0 · PDBe 6CI0 · UniProt P33517 · UniProt Q03736
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.