MolNFT v1 · #52712 · protein
Geobacillus stearothermophilus 6-phosphogluconate dehydrogenase with bound 6- phosphogluconate
2W8Z · 6-phosphogluconate dehydrogenase, decarboxylating: “Geobacillus stearothermophilus 6-phosphogluconate dehydrogenase with bound 6- phosphogluconate”. X-ray diffraction, 2 ligands (6PG, SO4), 7 pockets (best druggability 0.74). MolNFT…
- PDB
- 2W8Z
- Type
- protein
- Length
- 935 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phosphogluconate dehydrogenase, decarboxylating
- EC
- 1.1.1.44
- Ligands
- 6PG, SO4
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) | protein | 468 | 56% helix, 11% strand | — |
| B | 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) | protein | 467 | 56% helix, 10% strand | — |
Ligands and binding sites
- 6PG · 6-phosphogluconic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.74 | 0.98 | 22 | empty |
| 2 | 448 | 0.69 | 0.80 | 48 | 6PG |
| 3 | 513 | 0.69 | 0.79 | 58 | 6PG |
| 4 | 76 | 0.40 | 0.79 | 17 | empty |
| 5 | 96 | 0.40 | 0.77 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 5623 Ų buried · 58 hydrogen bonds · protein-protein
Compared structures
- 2W8Z · Geobacillus stearothermophilus 6-phosphogluconate dehydrogenase with bound 6… · 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
- Elsewhere: RCSB PDB 2W8Z · PDBe 2W8Z
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