MolNFT v2 · #117056 · protein
Crystal structure of IGPD from Pyrococcus furiosus in complex with (S)-C348
5DNL · Imidazoleglycerol-phosphate dehydratase: “Crystal structure of IGPD from Pyrococcus furiosus in complex with (S)-C348”. X-ray diffraction at 1.53, 2 ligands (5DL, MN), 4 pockets (best druggability 0.67). MolNFT v2 #117056 on…
- PDB
- 5DNL
- Type
- protein
- Length
- 528 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.53
- Source
- Pyrococcus furiosus
- Molecule
- Imidazoleglycerol-phosphate dehydratase
- EC
- 4.2.1.19
- UniProt
- P58880
- Ligands
- 5DL, MN
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · resolution 1.53 · 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
- 5DL · [(2S)-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 | 262 | 0.67 | 0.83 | 48 | 5DL |
| 2 | 146 | 0.50 | 0.79 | 21 | empty |
| 3 | 139 | 0.41 | 0.74 | 23 | empty |
| 4 | 76 | 0.34 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 770 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 660 Ų buried · 6 hydrogen bonds · protein-protein
- C–B · 512 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5DNL · Crystal structure of igpd from pyrococcus furiosus in complex with (S)-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 5DNL · PDBe 5DNL · UniProt P58880
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.