Research workbench
Crystal structure of the V465T mutant of 5-(HYDROXYMETHYL)FURFURAL oxidase (hmfo)
Analyse Crystal structure of the V465T mutant of 5-(HYDROXYMETHYL)FURFURAL oxidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F97
- Type
- protein
- Length
- 1,007 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-(HYDROXYMETHYL)FURFURAL oxidase
- EC
- 1.1.3.47, 1.8.3.-
- UniProt
- E4QP00
- Ligands
- FAD
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-(HYDROXYMETHYL)FURFURAL oxidase (EC 1.1.3.47, 1.8.3.-) | protein | 520 | 28% helix, 25% strand | E4QP00 |
| B | 5-(HYDROXYMETHYL)FURFURAL oxidase (EC 1.1.3.47, 1.8.3.-) | protein | 487 | 26% 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
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 956 | 0.84 | 0.85 | 83 | FAD |
| 2 | 1033 | 0.79 | 0.80 | 94 | empty |
| 3 | 678 | 0.78 | 0.83 | 83 | FAD |
| 4 | 241 | 0.54 | 0.76 | 31 | empty |
| 5 | 66 | 0.38 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 691 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6F97 · Crystal structure of the V465T mutant of 5-(Hydroxymethyl)furfural Oxidase (HMFO) · 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 6F97 · PDBe 6F97 · UniProt E4QP00
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