MolNFT v1 · #52713 · protein
Geobacillus stearothermophilus 6-phosphogluconate dehydrogenase with bound 6-phosphogluconate
2W90 · 6-phosphogluconate dehydrogenase, decarboxylating: “Geobacillus stearothermophilus 6-phosphogluconate dehydrogenase with bound 6-phosphogluconate”. X-ray diffraction, 2 ligands (6PG, SO4), 8 pockets (best druggability 0.73). MolNFT…
- PDB
- 2W90
- Type
- protein
- Length
- 941 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
- 8 · best druggability 0.73
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 | 470 | 56% helix, 10% strand | — |
| B | 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) | protein | 471 | 56% helix, 11% strand | — |
Ligands and binding sites
- 6PG · 6-phosphogluconic acid · ligand · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- 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
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.73 | 0.99 | 23 | empty |
| 2 | 430 | 0.69 | 0.80 | 43 | 6PG |
| 3 | 367 | 0.68 | 0.81 | 37 | SO4 |
| 4 | 121 | 0.42 | 0.76 | 29 | empty |
| 5 | 68 | 0.40 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 5681 Ų buried · 56 hydrogen bonds · protein-protein
Compared structures
- 2W90 · 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 2W90 · PDBe 2W90
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