MolNFT v1 · #25291 · protein
Crystal structure of gluconate 5-dehydrogenase (TM0441) from thermotoga maritima at 2.07 a resolution
1VL8: “Crystal structure of gluconate 5-dehydrogenase (TM0441) from thermotoga maritima at 2.07 a resolution”. X-ray diffraction, 3 ligands (NAP, MG, PO4), 3 pockets (best druggability 0.78). MolNFT v1 #25291 on GenesisL1: 3D structure…
- PDB
- 1VL8
- Type
- protein
- Length
- 503 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gluconate 5-dehydrogenase
- EC
- 1.1.1.69
- UniProt
- Q9WYS2
- Ligands
- NAP, MG, PO4
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gluconate 5-dehydrogenase (EC 1.1.1.69) | protein | 251 | 51% helix, 15% strand | Q9WYS2 |
| B | Gluconate 5-dehydrogenase (EC 1.1.1.69) | protein | 252 | 52% helix, 15% strand | Q9WYS2 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains B
- PO4 · Phosphate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.78 | 0.88 | 48 | NAP |
| 2 | 350 | 0.77 | 0.88 | 48 | NAP |
| 3 | 70 | 0.38 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1681 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1VL8 · Crystal structure of Gluconate 5-dehydrogenase (TM0441) from Thermotoga maritima at 2.07… · 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 Q9WYS2
- Elsewhere: RCSB PDB 1VL8 · PDBe 1VL8 · UniProt Q9WYS2
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