MolNFT v1 · #116773 · protein
Crystal structure of igpd from pyrococcus furiosus in complex with (R)-C348
5DNX · Imidazoleglycerol-phosphate dehydratase: “Crystal structure of igpd from pyrococcus furiosus in complex with (R)-C348”. X-ray diffraction, 2 ligands (5LD, MN), 4 pockets (best druggability 0.64). MolNFT v1 #116773 on GenesisL1: 3D…
- PDB
- 5DNX
- Type
- protein
- Length
- 528 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Imidazoleglycerol-phosphate dehydratase
- EC
- 4.2.1.19
- UniProt
- P58880
- Ligands
- 5LD, MN
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B | Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) | protein | 176 | 38% helix, 30% strand | P58880 |
Ligands and binding sites
- 5LD · [(2R)-2-hydroxy-3-(1H-1,2,4-triazol-1-yl)propyl]phosphonic acid · ligand · 3 copies · chains A, C, B
- MN · Manganese (II) ion · metal · 6 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.64 | 0.82 | 52 | 5LD |
| 2 | 153 | 0.51 | 0.79 | 21 | empty |
| 3 | 151 | 0.43 | 0.75 | 26 | empty |
| 4 | 102 | 0.34 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 781 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 661 Ų buried · 6 hydrogen bonds · protein-protein
- C–B · 516 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5DNX · Crystal structure of IGPD from Pyrococcus furiosus in complex with (R)-C348 · the same entry in another collection · chain A against A, TM-score 1.00
- P58880 · AlphaFold monomer V2.0 prediction for imidazoleglycerol-phosphate dehydratase (P58880) · 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 P58880
- Elsewhere: RCSB PDB 5DNX · PDBe 5DNX · UniProt P58880
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