MolNFT v1 · #33208 · protein
Sulfolobus solfataricus glucose dehydrogenase 1 in complex with NADP
2CDA: “Sulfolobus solfataricus glucose dehydrogenase 1 in complex with NADP”. X-ray diffraction, 2 ligands (NAP, ZN), 3 pockets (best druggability 0.83). MolNFT v1 #33208 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2CDA
- Type
- protein
- Length
- 719 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose dehydrogenase
- EC
- 1.1.1.47
- UniProt
- O93715
- Ligands
- NAP, ZN
- Pockets
- 3 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose dehydrogenase (EC 1.1.1.47) | protein | 360 | 34% helix, 26% strand | O93715 |
| B | Glucose dehydrogenase (EC 1.1.1.47) | protein | 359 | 34% helix, 26% strand | O93715 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.83 | 0.84 | 99 | empty |
| 2 | 515 | 0.69 | 0.79 | 55 | NAP, ZN |
| 3 | 513 | 0.68 | 0.79 | 53 | NAP |
Interfaces
1 interface between chains.
- A–B · 1154 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2CDA · Sulfolobus solfataricus Glucose Dehydrogenase 1 in complex with NADP · the same entry in another collection · chain A against A, TM-score 1.00
- O93715 · AlphaFold monomer V2.0 prediction for glucose 1-dehydrogenase (O93715) · a predicted model of the same protein · chain B 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 O93715
- Elsewhere: RCSB PDB 2CDA · PDBe 2CDA · UniProt O93715
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