Research workbench
Structural insights into cofactor and substrate selection by GOX0499
Analyse Structural insights into cofactor and substrate selection by GOX0499 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VZ0
- Type
- protein
- Length
- 1,824 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative NAD-dependent aldehyde dehydrogenase
- UniProt
- Q5FTL8
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative NAD-dependent aldehyde dehydrogenase | protein | 456 | 43% helix, 21% strand | Q5FTL8 |
Ligands and binding sites
- 2PE · Nonaethylene glycol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 205 | 0.81 | 0.95 | 26 | empty |
| 2 | 489 | 0.81 | 0.88 | 56 | empty |
| 3 | 725 | 0.79 | 0.83 | 78 | empty |
| 4 | 1157 | 0.76 | 0.78 | 131 | empty |
| 5 | 236 | 0.75 | 0.89 | 42 | 2PE |
Interfaces
5 interfaces between chains.
- A–B · 2407 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2338 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 612 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 531 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 12 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 modified (engineered).
Compared structures
- 3VZ0 · Structural insights into cofactor and substrate selection by Gox0499 · the same entry in another collection · 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 Q5FTL8
- Elsewhere: RCSB PDB 3VZ0 · PDBe 3VZ0 · UniProt Q5FTL8
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