MolNFT v1 · #41052 · protein
Crystal structure of choline oxidase reveals insights into the catalytic mechanism
2JBV: “Crystal structure of choline oxidase reveals insights into the catalytic mechanism”. X-ray diffraction, 2 ligands (FAO, UNX), 8 pockets (best druggability 0.87). MolNFT v1 #41052 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2JBV
- Type
- protein
- Length
- 1,057 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Choline oxidase
- EC
- 1.1.3.17
- UniProt
- Q7X2H8
- Ligands
- FAO, UNX
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Choline oxidase (EC 1.1.3.17) | protein | 527 | 26% helix, 25% strand | Q7X2H8 |
| B | Choline oxidase (EC 1.1.3.17) | protein | 530 | 27% helix, 25% strand | Q7X2H8 |
Ligands and binding sites
- FAO · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[(4aS,10aR)-7,8-dimethyl-2,4-dioxo-1,3,4,4a,5,10a-hexahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate · ligand · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 4 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.87 | 0.97 | 60 | FAO, DMS, UNX |
| 2 | 355 | 0.87 | 0.96 | 61 | FAO, DMS, UNX |
| 3 | 998 | 0.84 | 0.86 | 98 | empty |
| 4 | 360 | 0.66 | 0.80 | 50 | empty |
| 5 | 358 | 0.62 | 0.78 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1297 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2JBV · Crystal structure of choline oxidase reveals insights into the catalytic mechanism · the same entry in another collection · chain A against A, TM-score 1.00
- Q7X2H8 · AlphaFold monomer V2.0 prediction for choline oxidase (Q7X2H8) · a predicted model of the same protein · 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 Q7X2H8
- Elsewhere: RCSB PDB 2JBV · PDBe 2JBV · UniProt Q7X2H8
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