MolNFT v1 · #107552 · protein
Crystal structure of 5-hydroxymethylfurfural oxidase (hmfo) in the oxidized state
4UDP · Glucose-methanol-choline oxidoreductase: “Crystal structure of 5-hydroxymethylfurfural oxidase (hmfo) in the oxidized state”. X-ray diffraction, 1 ligand (FAD), 4 pockets (best druggability 0.85). MolNFT v1 #107552 on GenesisL1: 3D…
- PDB
- 4UDP
- Type
- protein
- Length
- 1,032 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-methanol-choline oxidoreductase
- UniProt
- E4QP00
- Ligands
- FAD
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose-methanol-choline oxidoreductase | protein | 520 | 28% helix, 25% strand | E4QP00 |
| B | Glucose-methanol-choline oxidoreductase | protein | 512 | 28% helix, 26% strand | E4QP00 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.85 | 0.87 | 89 | FAD |
| 2 | 902 | 0.85 | 0.86 | 100 | FAD |
| 3 | 947 | 0.79 | 0.81 | 91 | empty |
| 4 | 271 | 0.55 | 0.76 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 672 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4UDP · Crystal structure of 5-hydroxymethylfurfural oxidase (HMFO) in the oxidized state · the same entry in another collection · chain A against A, TM-score 1.00
- E4QP00 · AlphaFold monomer V2.0 prediction for 5-(HYDROXYMETHYL)FURFURAL oxidase (E4QP00) · a predicted model of the same protein · chain B 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 E4QP00
- Elsewhere: RCSB PDB 4UDP · PDBe 4UDP · UniProt E4QP00
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