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The crystal structure of indole-3-glycerol phosphate synthase from campylobacter jejuni subsp. jejuni nctc 11168
Analyse The crystal structure of indole-3-glycerol phosphate synthase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BMA
- Type
- protein
- Length
- 518 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Indole-3-glycerol phosphate synthase
- EC
- 4.1.1.48
- UniProt
- Q9PI11
- Ligands
- K, PO4, CL
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Indole-3-glycerol phosphate synthase (EC 4.1.1.48) | protein | 259 | 45% helix, 18% strand | Q9PI11 |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 9 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
- FMT · Formic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.80 | 0.96 | 27 | empty |
| 2 | 156 | 0.76 | 0.93 | 34 | PO4, ACT |
| 3 | 120 | 0.51 | 0.81 | 20 | empty |
| 4 | 52 | 0.50 | 0.87 | 17 | PO4 |
| 5 | 101 | 0.42 | 0.78 | 21 | PO4 |
Interfaces
1 interface between chains.
- A–B · 2232 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6BMA · The crystal structure of indole-3-glycerol phosphate synthase from Campylobacter jejuni… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9PI11 · AlphaFold monomer V2.0 prediction for indole-3-glycerol phosphate synthase (Q9PI11) · a predicted model of the same protein · chain A against A, TM-score 0.86
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 Q9PI11
- Elsewhere: RCSB PDB 6BMA · PDBe 6BMA · UniProt Q9PI11
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