Research workbench
Towards understanding the mechanism of the complex cyclization reaction catalyzed by imidazole glycerophosphate synthase
Analyse Towards understanding the mechanism of the complex cyclization reaction… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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