Research workbench
An unexpected outcome of surface-engineering an integral membrane protein: improved crystallization of cytochrome BA3 oxidase from thermus thermophilus
Analyse An unexpected outcome of surface-engineering an integral membrane protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QPD
- Type
- protein
- Length
- 756 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, CU1
- Pockets
- 6 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 61% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C oxidase subunit 1 (EC 1.9.3.1) | protein | 557 | 70% helix, 1% strand | Q5SJ79 |
| B | Cytochrome C oxidase subunit 2 (EC 1.9.3.1) | protein | 166 | 28% helix, 30% 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
- CU1 · Copper (I) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1087 | 0.90 | 0.91 | 132 | HEM, HAS |
| 2 | 121 | 0.65 | 0.88 | 20 | empty |
| 3 | 75 | 0.40 | 0.78 | 16 | empty |
| 4 | 98 | 0.37 | 0.75 | 20 | empty |
| 5 | 82 | 0.35 | 0.74 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2977 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 1041 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 899 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2QPD · An unexpected outcome of surface-engineering an integral membrane protein: Improved… · 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 0.98
- 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 0.81
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 2QPD · PDBe 2QPD · UniProt Q5SJ79 · UniProt Q5SJ80 · UniProt P82543
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