MolNFT v1 · #7434 · protein
Crystal structure of glucose dehydrogenase mutant E96A complexed with NAD+
1G6K · Glucose 1-dehydrogenase: “Crystal structure of glucose dehydrogenase mutant E96A complexed with NAD+”. X-ray diffraction, 1 ligand (NAD), 7 pockets (best druggability 0.74). MolNFT v1 #7434 on GenesisL1: 3D structure, binding sites…
- PDB
- 1G6K
- Type
- protein
- Length
- 1,044 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose 1-dehydrogenase
- EC
- 1.1.1.47
- UniProt
- P40288
- Ligands
- NAD
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F | Glucose 1-dehydrogenase (EC 1.1.1.47) | protein | 261 | 52% helix, 15% strand | P40288 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 742 | 0.74 | 0.79 | 60 | NAD |
| 2 | 784 | 0.74 | 0.79 | 65 | NAD |
| 3 | 729 | 0.74 | 0.79 | 65 | NAD |
| 4 | 715 | 0.73 | 0.79 | 55 | NAD |
| 5 | 53 | 0.40 | 0.81 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1601 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1585 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1G6K · Crystal structure of glucose dehydrogenase mutant E96A complexed with NAD+ · the same entry in another collection · chain F against F, TM-score 1.00
- P40288 · AlphaFold monomer V2.0 prediction for glucose 1-dehydrogenase (P40288) · a predicted model of the same protein · chain E 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 P40288
- Elsewhere: RCSB PDB 1G6K · PDBe 1G6K · UniProt P40288
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