MolNFT v1 · #20543 · protein
Crystal structure of imidazole glycerol phosphate dehydratase
1RHY: “Crystal structure of imidazole glycerol phosphate dehydratase”. X-ray diffraction, 3 ligands (EMC, HG, SO4), 4 pockets (best druggability 0.56). MolNFT v1 #20543 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1RHY
- Type
- protein
- Length
- 360 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Imidazole glycerol phosphate dehydratase
- EC
- 4.2.1.19
- UniProt
- P40919
- Ligands
- EMC, HG, SO4
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Imidazole glycerol phosphate dehydratase (EC 4.2.1.19) | protein | 180 | 34% helix, 32% strand | P40919 |
| B | Imidazole glycerol phosphate dehydratase (EC 4.2.1.19) | protein | 180 | 37% helix, 32% strand | P40919 |
Ligands and binding sites
- EMC · Ethyl mercury ion · ligand · 4 copies · chains A, B
- HG · Mercury (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
- ACY · Acetic acid · additive · 7 copies · chains A, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.56 | 0.82 | 30 | empty |
| 2 | 159 | 0.50 | 0.78 | 27 | HG, EMC |
| 3 | 51 | 0.47 | 0.85 | 20 | empty |
| 4 | 50 | 0.29 | 0.75 | 15 | EMC |
Interfaces
1 interface between chains.
- A–B · 853 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1RHY · Crystal structure of Imidazole Glycerol Phosphate Dehydratase · the same entry in another collection · 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 P40919
- Elsewhere: RCSB PDB 1RHY · PDBe 1RHY · UniProt P40919
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