MolNFT v1 · #11741 · protein
Crystal structure of imidazole glycerol phosphate synthase: a tunnel through a (BETA/ALPHA)8 barrel joins two active sites
1JVN · Bifunctional histidine biosynthesis protein hishf: “Crystal structure of imidazole glycerol phosphate synthase: a tunnel through a (BETA/ALPHA)8 barrel joins two…”. X-ray diffraction, 3 ligands (POP, NI, SO4), 14 pockets (best…
- PDB
- 1JVN
- Type
- protein
- Length
- 1,074 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional histidine biosynthesis protein hishf
- EC
- 2.4.2.-
- UniProt
- P33734
- Ligands
- POP, NI, SO4
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bifunctional histidine biosynthesis protein hishf (EC 2.4.2.-) | protein | 537 | 33% helix, 25% strand | P33734 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · chains B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.77 | 0.98 | 19 | empty |
| 2 | 71 | 0.76 | 0.99 | 20 | empty |
| 3 | 533 | 0.66 | 0.77 | 67 | SO4, POP |
| 4 | 404 | 0.62 | 0.77 | 50 | SO4 |
| 5 | 52 | 0.42 | 0.83 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 513 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 1JVN · Crystal structure of imidazole glycerol phosphate synthase: a tunnel through a… · 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 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 P33734
- Elsewhere: RCSB PDB 1JVN · PDBe 1JVN · UniProt P33734
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