MolNFT v1 · #17555 · protein
Towards understanding the mechanism of the complex cyclization reaction catalyzed by imidazole glycerophosphate synthase
1OX5 · Imidazole glycerol phosphate synthase hishf: “Towards understanding the mechanism of the complex cyclization reaction catalyzed by imidazole…”. X-ray diffraction, 2 ligands (1PR, NI), 13 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 1OX5
- Type
- protein
- Length
- 1,059 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Imidazole glycerol phosphate synthase hishf
- EC
- 2.4.2.-, 4.1.3.-
- UniProt
- P33734
- Ligands
- 1PR, NI
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Imidazole glycerol phosphate synthase hishf (EC 2.4.2.-, 4.1.3.-) | protein | 532 | 33% helix, 24% strand | P33734 |
| B | Imidazole glycerol phosphate synthase hishf (EC 2.4.2.-, 4.1.3.-) | protein | 527 | 34% helix, 24% strand | P33734 |
Ligands and binding sites
- 1PR · Phosphoric acid mono-[5-({[5-carbamoyl-3-(5-phosphonooxy-5-deoxy-ribofuranosyl)- 3H-imidazol-4-ylamino]-methyl}-amino)-2,3,4-trihydroxy-pentyl] ester · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.76 | 0.99 | 19 | empty |
| 2 | 68 | 0.75 | 0.99 | 19 | empty |
| 3 | 359 | 0.68 | 0.82 | 42 | 1PR |
| 4 | 404 | 0.64 | 0.78 | 50 | 1PR |
| 5 | 112 | 0.38 | 0.75 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 510 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 1OX5 · Towards understanding the mechanism of the complex cyclization reaction catalyzed by… · the same entry in another collection · chain A against A, TM-score 1.00
- P33734 · AlphaFold monomer V2.0 prediction for imidazole glycerol phosphate synthase hishf (P33734) · 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 P33734
- Elsewhere: RCSB PDB 1OX5 · PDBe 1OX5 · UniProt P33734
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