MolNFT v1 · #18175 · protein
X-ray structure of 6-phosphogluconate dehydrogenase from the protozoan parasite T. brucei
1PGJ: “X-ray structure of 6-phosphogluconate dehydrogenase from the protozoan parasite T. brucei”. X-ray diffraction, 1 ligand (SO4), 12 pockets (best druggability 0.73). MolNFT v1 #18175 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1PGJ
- Type
- protein
- Length
- 956 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phosphogluconate dehydrogenase
- EC
- 1.1.1.44
- UniProt
- P31072
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 6-phosphogluconate dehydrogenase (EC 1.1.1.44) | protein | 478 | 56% helix, 10% strand | P31072 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.73 | 0.88 | 33 | SO4 |
| 2 | 323 | 0.72 | 0.85 | 33 | SO4 |
| 3 | 61 | 0.72 | 0.98 | 24 | empty |
| 4 | 119 | 0.37 | 0.74 | 17 | empty |
| 5 | 80 | 0.37 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 6424 Ų buried · 99 hydrogen bonds · protein-protein
Compared structures
- 1PGJ · X-ray structure of 6-phosphogluconate dehydrogenase from the protozoan parasite T. brucei · the same entry in another collection · chain A against A, TM-score 1.00
- P31072 · AlphaFold monomer V2.0 prediction for 6-phosphogluconate dehydrogenase, decarboxylating… · a predicted model of the same protein · chain B 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 P31072
- Elsewhere: RCSB PDB 1PGJ · PDBe 1PGJ · UniProt P31072
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