Research workbench
Crystal structure of the aberrant BA3-cytochrome-C oxidase from thermus thermophilus
Analyse Crystal structure of the aberrant BA3-cytochrome-C oxidase from thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EHK
- Type
- protein
- Length
- 743 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BA3-type cytochrome-C oxidase
- EC
- 1.9.3.1
- UniProt
- Q5SJ79, Q5SJ80, P82543
- Ligands
- BNG, HEM, HAS, CUA, CU
- Pockets
- 5 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 63% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BA3-type cytochrome-C oxidase (EC 1.9.3.1) | protein | 544 | 74% helix, 2% strand | Q5SJ79 |
| B | BA3-type cytochrome-C oxidase (EC 1.9.3.1) | protein | 166 | 26% helix, 35% strand | Q5SJ80 |
| C | BA3-type cytochrome-C oxidase (EC 1.9.3.1) | protein | 33 | 82% helix, 0% strand | P82543 |
Ligands and binding sites
- BNG · nonyl beta-D-glucopyranoside · ligand · 3 copies · chains A, B, C
- 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.90 | 0.91 | 132 | CU, HEM, HAS |
| 2 | 95 | 0.39 | 0.76 | 18 | empty |
| 3 | 84 | 0.36 | 0.74 | 21 | empty |
| 4 | 71 | 0.32 | 0.74 | 20 | empty |
| 5 | 63 | 0.29 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2977 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1065 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 911 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1EHK · Crystal structure of the aberrant BA3-cytochrome-C oxidase from thermus thermophilus · 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 1.00
- 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 0.83
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 1EHK · PDBe 1EHK · UniProt Q5SJ79 · UniProt Q5SJ80 · UniProt P82543
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