MolNFT v1 · #52301 · protein
Haloferax mediterranei glucose dehydrogenase in complex with NADPH and zn.
2VWP: “Haloferax mediterranei glucose dehydrogenase in complex with NADPH and zn.”. X-ray diffraction, 2 ligands (NDP, ZN), 3 pockets (best druggability 0.67). MolNFT v1 #52301 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2VWP
- Type
- protein
- Length
- 357 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose dehydrogenase
- EC
- 1.1.1.47
- UniProt
- Q977U7
- Ligands
- NDP, ZN
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose dehydrogenase (EC 1.1.1.47) | protein | 357 | 32% helix, 27% strand | Q977U7 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.67 | 0.77 | 53 | NDP, ZN |
| 2 | 188 | 0.45 | 0.74 | 27 | empty |
| 3 | 77 | 0.32 | 0.74 | 17 | empty |
Compared structures
- 2VWP · Haloferax mediterranei glucose dehydrogenase in complex with NADPH and Zn. · the same entry in another collection · chain A against A, TM-score 1.00
- Q977U7 · AlphaFold monomer V2.0 prediction for glucose 1-dehydrogenase (Q977U7) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q977U7
- Elsewhere: RCSB PDB 2VWP · PDBe 2VWP · UniProt Q977U7
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