Research workbench
Structure refinement of the aldehyde oxidoreductase from desulfovibrio gigas at 1.28 a
Analyse Structure refinement of the aldehyde oxidoreductase from desulfovibrio gigas at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VLB
- Type
- protein
- Length
- 907 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde oxidoreductase
- EC
- 1.2.3.1
- UniProt
- Q46509
- Ligands
- FES, PCD, MG, CL
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aldehyde oxidoreductase (EC 1.2.3.1) | protein | 907 | 33% helix, 23% strand | Q46509 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A
- PCD · (molybdopterin-cytosine dinucleotide-S,S)-dioxo-aqua-molybdenum(v) · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- IPA · Isopropyl alcohol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.81 | 0.88 | 83 | PCD, IPA |
| 2 | 156 | 0.55 | 0.81 | 25 | empty |
| 3 | 89 | 0.44 | 0.80 | 25 | empty |
| 4 | 88 | 0.36 | 0.75 | 20 | empty |
| 5 | 81 | 0.35 | 0.75 | 14 | empty |
Compared structures
- 1VLB · Structure refinement of the aldehyde oxidoreductase from desulfovibrio gigas at 1.28 a · the same entry in another collection · chain A against A, TM-score 1.00
- Q46509 · AlphaFold monomer V2.0 prediction for aldehyde oxidoreductase (Q46509) · 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 Q46509
- Elsewhere: RCSB PDB 1VLB · PDBe 1VLB · UniProt Q46509
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