Research workbench
Structure of thermoplasma volcanium aldohexose dehydrogenase
Analyse Structure of thermoplasma volcanium aldohexose dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VTZ
- Type
- protein
- Length
- 1,010 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose 1-dehydrogenase
- EC
- 1.1.1.118
- UniProt
- Q97CM7
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose 1-dehydrogenase (EC 1.1.1.118) | protein | 253 | 49% helix, 16% strand | Q97CM7 |
| B | Glucose 1-dehydrogenase (EC 1.1.1.118) | protein | 253 | 49% helix, 16% strand | Q97CM7 |
| C, D | Glucose 1-dehydrogenase (EC 1.1.1.118) | protein | 252 | 50% helix, 17% strand | Q97CM7 |
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 768 | 0.86 | 0.89 | 77 | empty |
| 2 | 407 | 0.77 | 0.86 | 50 | empty |
| 3 | 387 | 0.77 | 0.86 | 48 | empty |
| 4 | 418 | 0.76 | 0.85 | 50 | empty |
| 5 | 374 | 0.76 | 0.86 | 52 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1698 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 1688 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 1484 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1478 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1414 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3VTZ · Structure of Thermoplasma volcanium aldohexose dehydrogenase · 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 Q97CM7
- Elsewhere: RCSB PDB 3VTZ · PDBe 3VTZ · UniProt Q97CM7
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