MolNFT v1 · #61720 · protein
Catalytic core subunits (I and II) of cytochrome C oxidase from rhodobacter sphaeroides complexed with deoxycholic acid
3DTU · Cytochrome C oxidase subunit 1: “Catalytic core subunits (I and II) of cytochrome C oxidase from rhodobacter sphaeroides complexed with…”. X-ray diffraction, 10 ligands (TRD, HEA, HTO), 14 pockets (best druggability 0.90). MolNFT v1…
- PDB
- 3DTU
- Type
- protein
- Length
- 1,592 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, DXC, CU, CD, MG, CA, OH, PO4
- Pockets
- 14 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C oxidase subunit 1 (EC 1.9.3.1) | protein | 539 | 72% helix, 2% strand | P33517 |
| B | Cytochrome C oxidase subunit 2 (EC 1.9.3.1) | protein | 259 | 37% helix, 25% strand | Q03736 |
| C | Cytochrome C oxidase subunit 1 (EC 1.9.3.1) | protein | 536 | 71% helix, 2% strand | P33517 |
| D | Cytochrome C oxidase subunit 2 (EC 1.9.3.1) | protein | 258 | 37% helix, 25% strand | Q03736 |
Ligands and binding sites
- TRD · Tridecane · ligand · 23 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
- DXC · (3alpha,5beta,12alpha)-3,12-dihydroxycholan-24-oic acid · ligand · chains C, D
- CU · Copper (II) ion · metal · 6 copies · chains A, B, C, D
- CD · Cadmium ion · metal · 5 copies · chains B, D
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, C
- OH · Hydroxide ion · ion · 2 copies · chains A, C
- PO4 · Phosphate ion · ion · 2 copies · chains A, C
- DMU · Decyl-beta-D-maltopyranoside · additive · 9 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1144 | 0.90 | 0.91 | 126 | DMU, OH, HEA, TRD |
| 2 | 1190 | 0.88 | 0.89 | 128 | OH, HEA, TRD |
| 3 | 671 | 0.72 | 0.79 | 50 | TRD, CD |
| 4 | 336 | 0.68 | 0.81 | 26 | TRD |
| 5 | 317 | 0.66 | 0.81 | 26 | TRD |
Interfaces
4 interfaces between chains.
- C–D · 4033 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 4012 Ų buried · 48 hydrogen bonds · protein-protein
- A–D · 243 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 178 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3DTU · 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 D 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 3DTU · PDBe 3DTU · UniProt P33517 · UniProt Q03736
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