Research workbench
Crystal structure of choline oxidase in complex with the reaction product glycine betaine
Analyse Crystal structure of choline oxidase in complex with the reaction product… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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