MolNFT v1 · #107554 · protein
Crystal structure of the H467A mutant of 5- hydroxymethylfurfural oxidase (hmfo)
4UDR · Glucose-methanol-choline oxidoreductase: “Crystal structure of the H467A mutant of 5- hydroxymethylfurfural oxidase (hmfo)”. X-ray diffraction, 1 ligand (FAD), 6 pockets (best druggability 0.86). MolNFT v1 #107554 on GenesisL1: 3D…
- PDB
- 4UDR
- Type
- protein
- Length
- 1,050 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
- 6 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glucose-methanol-choline oxidoreductase | protein | 525 | 28% helix, 25% strand | E4QP00 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 918 | 0.86 | 0.87 | 100 | FAD |
| 2 | 910 | 0.86 | 0.87 | 100 | FAD |
| 3 | 1007 | 0.78 | 0.80 | 86 | empty |
| 4 | 273 | 0.55 | 0.76 | 32 | empty |
| 5 | 82 | 0.41 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 640 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4UDR · Crystal structure of the H467A mutant of 5-hydroxymethylfurfural oxidase (HMFO) · the same entry in another collection · chain B against B, TM-score 1.00
- E4QP00 · AlphaFold monomer V2.0 prediction for 5-(HYDROXYMETHYL)FURFURAL oxidase (E4QP00) · 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 E4QP00
- Elsewhere: RCSB PDB 4UDR · PDBe 4UDR · UniProt E4QP00
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