MolNFT v1 · #99978 · protein
Crystal structure of choline oxidase in complex with the reaction product glycine betaine
4MJW: “Crystal structure of choline oxidase in complex with the reaction product glycine betaine”. X-ray diffraction, 2 ligands (FAD, BET), 10 pockets (best druggability 0.88). MolNFT v1 #99978 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4MJW
- Type
- protein
- Length
- 1,063 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
- FAD, BET
- Pockets
- 10 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Choline oxidase (EC 1.1.3.17) | protein | 532 | 27% helix, 25% strand | Q7X2H8 |
| B | Choline oxidase (EC 1.1.3.17) | protein | 531 | 27% helix, 24% strand | Q7X2H8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- BET · Trimethyl glycine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 631 | 0.88 | 0.93 | 94 | FAD, BET |
| 2 | 448 | 0.87 | 0.94 | 75 | FAD, BET |
| 3 | 59 | 0.72 | 0.98 | 18 | empty |
| 4 | 51 | 0.71 | 0.98 | 18 | empty |
| 5 | 61 | 0.59 | 0.91 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1108 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 4MJW · Crystal Structure of Choline Oxidase in Complex with the Reaction Product Glycine Betaine · the same entry in another collection · chain B against B, TM-score 1.00
- Q7X2H8 · AlphaFold monomer V2.0 prediction for choline oxidase (Q7X2H8) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 4MJW · PDBe 4MJW · UniProt Q7X2H8
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