Research workbench
Structure of recombinant cytochrome BA3 oxidase from thermus thermophilus
Analyse Structure of recombinant cytochrome BA3 oxidase from thermus thermophilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XME
- Type
- protein
- Length
- 756 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C oxidase polypeptide I; Cytochrome C oxidase polypeptide II; Cytochrome C…
- EC
- 1.9.3.1
- UniProt
- Q56408, P98052, P82543
- Ligands
- BNG, HEM, HAS, CUA, CU
- Pockets
- 5 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C oxidase polypeptide I (EC 1.9.3.1) | protein | 557 | 74% helix, 2% strand | Q56408 |
| B | Cytochrome C oxidase polypeptide II (EC 1.9.3.1) | protein | 166 | 27% helix, 35% strand | P98052 |
| C | Cytochrome C oxidase polypeptide iia (EC 1.9.3.1) | protein | 33 | 82% helix, 0% strand | P82543 |
Ligands and binding sites
- BNG · nonyl beta-D-glucopyranoside · ligand · chains A
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- HAS · Heme-as · ligand · chains A, C
- CUA · Dinuclear copper ion · ligand · chains B
- CU · Copper (II) ion · metal · chains A
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.90 | 0.91 | 142 | HEM, HAS, GOL |
| 2 | 58 | 0.71 | 0.97 | 19 | empty |
| 3 | 83 | 0.37 | 0.76 | 24 | empty |
| 4 | 88 | 0.35 | 0.74 | 18 | empty |
| 5 | 63 | 0.28 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2950 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1083 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 949 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1XME · Structure of Recombinant Cytochrome ba3 Oxidase from Thermus thermophilus · the same entry in another collection · chain A against A, TM-score 1.00
- P82543 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase polypeptide 2A (P82543) · a predicted model of the same protein · chain C against A, TM-score 0.83
- P98052 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit 2 (P98052) · a predicted model of the same protein · chain B against A, TM-score 0.76
- Q56408 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit 1 (Q56408) · a predicted model of the same protein · chain A against A, TM-score 0.19
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 Q56408
- Every structure of UniProt P98052
- Every structure of UniProt P82543
- Elsewhere: RCSB PDB 1XME · PDBe 1XME · UniProt Q56408 · UniProt P98052 · UniProt P82543
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