Research workbench
Structure of thermus thermophilus cytochrome BA3 oxidase 120S after xe depressurization
Analyse Structure of thermus thermophilus cytochrome BA3 oxidase 120S after xe… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S3A
- Type
- protein
- Length
- 753 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C oxidase subunit 1; Cytochrome C oxidase subunit 2; Cytochrome C oxidase…
- EC
- 1.9.3.1
- UniProt
- Q5SJ79, Q5SJ80, P82543
- Ligands
- HEM, HAS, CUA, CU, XE
- Pockets
- 5 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 62% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C oxidase subunit 1 (EC 1.9.3.1) | protein | 554 | 72% helix, 2% strand | Q5SJ79 |
| B | Cytochrome C oxidase subunit 2 (EC 1.9.3.1) | protein | 166 | 24% helix, 33% strand | Q5SJ80 |
| C | Cytochrome C oxidase polypeptide 2A (EC 1.9.3.1) | protein | 33 | 82% helix, 0% strand | P82543 |
Ligands and binding sites
- 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
- XE · Xenon · ion · 4 copies · chains A
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 | 882 | 0.89 | 0.91 | 94 | HEM, HAS |
| 2 | 182 | 0.80 | 0.94 | 36 | XE |
| 3 | 68 | 0.44 | 0.81 | 21 | empty |
| 4 | 97 | 0.40 | 0.75 | 17 | empty |
| 5 | 60 | 0.29 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3039 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 1102 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 917 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3S3A · Structure of Thermus thermophilus cytochrome ba3 oxidase 120s after Xe depressurization · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SJ79 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit 1 (Q5SJ79) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q5SJ80 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit 2 (Q5SJ80) · a predicted model of the same protein · chain B against A, TM-score 0.99
- 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 0.82
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 Q5SJ79
- Every structure of UniProt Q5SJ80
- Every structure of UniProt P82543
- Elsewhere: RCSB PDB 3S3A · PDBe 3S3A · UniProt Q5SJ79 · UniProt Q5SJ80 · UniProt P82543
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