MolNFT v1 · #18177 · protein
Crystallographic study of coenzyme, coenzyme analogue and substrate binding in 6-phosphogluconate dehydrogenase: implications for NADP specificity and the enzyme mechanism
1PGN: “Crystallographic study of coenzyme, coenzyme analogue and substrate binding in 6-phosphogluconate…”. X-ray diffraction, 3 ligands (NBP, POP, SO4), 2 pockets (best druggability 0.62). MolNFT v1 #18177 on GenesisL1: 3D structure…
- PDB
- 1PGN
- Type
- protein
- Length
- 473 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phosphogluconate dehydrogenase
- EC
- 1.1.1.44
- UniProt
- P00349
- Ligands
- NBP, POP, SO4
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-phosphogluconate dehydrogenase (EC 1.1.1.44) | protein | 473 | 57% helix, 10% strand | P00349 |
Ligands and binding sites
- NBP · Nicotinamide 8-bromo-adenine dinucleotide phosphate · ligand · chains A
- POP · Pyrophosphate 2- · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.62 | 0.75 | 35 | empty |
| 2 | 191 | 0.45 | 0.74 | 26 | SO4, NBP, POP |
Compared structures
- 1PGN · Crystallographic study of coenzyme, coenzyme analogue and substrate binding in… · the same entry in another collection · chain A against A, TM-score 1.00
- P00349 · AlphaFold monomer V2.0 prediction for 6-phosphogluconate dehydrogenase, decarboxylating… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P00349
- Elsewhere: RCSB PDB 1PGN · PDBe 1PGN · UniProt P00349
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