Research workbench
A novel membrane-bound 6-phosphogluconate dehydrogenase from the acetic acid bacteria gluconacetobacter diazotrophicus (GD6PGD)
Analyse A novel membrane-bound 6-phosphogluconate dehydrogenase from the acetic acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VPB
- Type
- protein
- Length
- 644 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phosphogluconate dehydrogenase
- UniProt
- A9H324
- Ligands
- MG
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-phosphogluconate dehydrogenase | protein | 320 | 52% helix, 12% strand | A9H324 |
| B | 6-phosphogluconate dehydrogenase | protein | 324 | 52% helix, 12% strand | A9H324 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B
- PEG · Di(hydroxyethyl)ether · additive · chains A
- IPA · Isopropyl alcohol · additive
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.57 | 0.75 | 29 | empty |
| 2 | 311 | 0.57 | 0.76 | 30 | empty |
| 3 | 232 | 0.47 | 0.74 | 36 | empty |
| 4 | 73 | 0.30 | 0.73 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 3627 Ų buried · 48 hydrogen bonds · protein-protein
Compared structures
- 6VPB · A novel membrane-bound 6-phosphogluconate dehydrogenase from the acetic acid bacteria… · 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 A9H324
- Elsewhere: RCSB PDB 6VPB · PDBe 6VPB · UniProt A9H324
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.