MolNFT v1 · #64209 · protein
Dimeric 6-phosphogluconate dehydrogenase complexed with 6- phosphogluconate and 2'-monophosphoadenosine-5'-diphosphate
3FWN · 6-phosphogluconate dehydrogenase, decarboxylating: “Dimeric 6-phosphogluconate dehydrogenase complexed with 6- phosphogluconate and…”. X-ray diffraction, 2 ligands (6PG, ATR), 6 pockets (best druggability 0.80). MolNFT v1 #64209 on…
- PDB
- 3FWN
- Type
- protein
- Length
- 934 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
- UniProt
- P00350
- Ligands
- 6PG, ATR
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) | protein | 467 | 57% helix, 10% strand | P00350 |
Ligands and binding sites
- 6PG · 6-phosphogluconic acid · ligand · 2 copies · chains A, B
- ATR · 2'-monophosphoadenosine-5'-diphosphate · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 122 | 0.80 | 0.98 | 39 | empty |
| 2 | 431 | 0.71 | 0.82 | 50 | ATR, 6PG |
| 3 | 396 | 0.68 | 0.81 | 50 | 6PG |
| 4 | 176 | 0.46 | 0.75 | 23 | empty |
| 5 | 157 | 0.44 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 5592 Ų buried · 60 hydrogen bonds · protein-protein
Compared structures
- 3FWN · Dimeric 6-phosphogluconate dehydrogenase complexed with 6-phosphogluconate and… · the same entry in another collection · chain A against A, TM-score 1.00
- P00350 · AlphaFold monomer V2.0 prediction for 6-phosphogluconate dehydrogenase, decarboxylating… · a predicted model of the same protein · 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 P00350
- Elsewhere: RCSB PDB 3FWN · PDBe 3FWN · UniProt P00350
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