Research workbench
Structure of the H61T mutant of the flavoenzyme vanillyl-alcohol oxidase in the apo form complexed by ADP
Analyse Structure of the H61T mutant of the flavoenzyme vanillyl-alcohol oxidase in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1E8H
- Type
- protein
- Length
- 1,090 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vanillyl-alcohol oxidase
- EC
- 1.1.3.7
- UniProt
- P56216
- Ligands
- ADP
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Vanillyl-alcohol oxidase (EC 1.1.3.7) | protein | 545 | 38% helix, 18% strand | P56216 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 761 | 0.86 | 0.89 | 77 | ADP |
| 2 | 776 | 0.85 | 0.88 | 77 | ADP |
| 3 | 1173 | 0.85 | 0.85 | 98 | empty |
| 4 | 54 | 0.44 | 0.84 | 15 | empty |
| 5 | 109 | 0.43 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 4153 Ų buried · 48 hydrogen bonds · protein-protein
Compared structures
- 1E8H · Structure of the H61T mutant of the flavoenzyme vanillyl-alcohol oxidase in the apo form… · the same entry in another collection · chain A against A, TM-score 1.00
- P56216 · AlphaFold monomer V2.0 prediction for vanillyl-alcohol oxidase (P56216) · 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 P56216
- Elsewhere: RCSB PDB 1E8H · PDBe 1E8H · UniProt P56216
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