MolNFT v1 · #74096 · protein
Catalytic core subunits (I and II) of cytochrome C oxidase from rhodobacter sphaeroides with D132A mutation in the reduced state
3OMN · Cytochrome C oxidase, AA3 type, subunit I: “Catalytic core subunits (I and II) of cytochrome C oxidase from rhodobacter sphaeroides with D132A mutation…”. X-ray diffraction, 9 ligands (TRD, HEA, HTH), 13 pockets (best druggability…
- PDB
- 3OMN
- Type
- protein
- Length
- 1,578 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C oxidase, AA3 type, subunit I; Cytochrome C oxidase subunit 2
- EC
- 1.9.3.1
- UniProt
- Q3J5A7, Q3J5G0
- Ligands
- TRD, HEA, HTH, CU1, CD, MG, CA, OH, CL
- Pockets
- 13 · 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, AA3 type, subunit I (EC 1.9.3.1) | protein | 535 | 72% helix, 2% strand | Q3J5A7 |
| B, D | Cytochrome C oxidase subunit 2 (EC 1.9.3.1) | protein | 256 | 38% helix, 25% strand | Q3J5G0 |
| C | Cytochrome C oxidase, AA3 type, subunit I (EC 1.9.3.1) | protein | 531 | 71% helix, 2% strand | Q3J5A7 |
Ligands and binding sites
- TRD · Tridecane · ligand · 9 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 · 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
- OH · Hydroxide ion · ion · 2 copies · chains A, C
- CL · Chloride ion · ion · 2 copies · chains A, C
- DMU · Decyl-beta-D-maltopyranoside · additive · 11 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.90 | 0.91 | 116 | OH, DMU, HEA |
| 2 | 1197 | 0.90 | 0.91 | 120 | OH, HEA |
| 3 | 324 | 0.66 | 0.80 | 27 | empty |
| 4 | 321 | 0.64 | 0.79 | 30 | TRD |
| 5 | 118 | 0.52 | 0.81 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–B · 4004 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 3996 Ų buried · 51 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3OMN · Catalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q3J5A7
- Every structure of UniProt Q3J5G0
- Elsewhere: RCSB PDB 3OMN · PDBe 3OMN · UniProt Q3J5A7 · UniProt Q3J5G0
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