Research workbench
Sulfolobus solfataricus glucose dehydrogenase 1 in complex with NADP and glucose
Analyse Sulfolobus solfataricus glucose dehydrogenase 1 in complex with NADP and glucose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CDB
- Type
- protein
- Length
- 1,436 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose 1-dehydrogenase (dhg-1)
- EC
- 1.1.1.47
- UniProt
- O93715
- Ligands
- NAP, BGC, ZN
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose 1-dehydrogenase (dhg-1) (EC 1.1.1.47) | protein | 360 | 35% helix, 28% strand | O93715 |
| B, D | Glucose 1-dehydrogenase (dhg-1) (EC 1.1.1.47) | protein | 359 | 35% helix, 27% strand | O93715 |
| C | Glucose 1-dehydrogenase (dhg-1) (EC 1.1.1.47) | protein | 358 | 34% helix, 29% strand | O93715 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, C, B, D
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, C, B, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.87 | 0.88 | 115 | empty |
| 2 | 669 | 0.73 | 0.80 | 73 | BGC, NAP |
| 3 | 659 | 0.73 | 0.80 | 62 | BGC, NAP |
| 4 | 687 | 0.72 | 0.79 | 67 | BGC, NAP |
| 5 | 649 | 0.72 | 0.79 | 65 | BGC, NAP |
Interfaces
6 interfaces between chains.
- B–D · 2291 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 2282 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1149 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1133 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 132 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2CDB · Sulfolobus solfataricus Glucose Dehydrogenase 1 in complex with NADP and glucose · the same entry in another collection · chain D against D, TM-score 1.00
- O93715 · AlphaFold monomer V2.0 prediction for glucose 1-dehydrogenase (O93715) · a predicted model of the same protein · chain D 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 2CDB · PDBe 2CDB · UniProt O93715
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