Research workbench
Igps (indole-3-glycerol phosphate synthase) from pseudomonas aeruginosa in complex with substrate inhibitor rcdrp
Analyse Igps (indole-3-glycerol phosphate synthase) from pseudomonas aeruginosa in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y88
- Type
- protein
- Length
- 2,105 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Indole-3-glycerol phosphate synthase; Indole-3-glycerol phosphate…
- EC
- 4.1.1.48
- UniProt
- A0A367MAM9
- Ligands
- 137, PO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Indole-3-glycerol phosphate synthase (EC 4.1.1.48) | protein | 264 | 47% helix, 17% strand | A0A367MAM9 |
| B, E, F | Indole-3-glycerol phosphate synthase (EC 4.1.1.48) | protein | 265 | 47% helix, 18% strand | A0A367MAM9 |
| C, H | Indole-3-glycerol phosphate synthase (EC 4.1.1.48) | protein | 264 | 47% helix, 18% strand | A0A367MAM9 |
| D | Indole-3-glycerol phosphate synthase (EC 4.1.1.48) | protein | 265 | 47% helix, 17% strand | A0A367MAM9 |
| G | Indole-3-glycerol phosphate SYNTHASE,INDOLE-3-glycerol phosphate synthase (EC 4.1.1.48) | protein | 253 | 46% helix, 17% strand | A0A367MAM9 |
Ligands and binding sites
- 137 · 1-(O-carboxy-phenylamino)-1-deoxy-D-ribulose-5-phosphate · ligand · 7 copies · chains A, B, C, D, E, F, H
- PO4 · Phosphate ion · ion · chains G
- GOL · Glycerol · additive · 7 copies · chains A, B, C, E, H
- CIT · Citric acid · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1032 | 0.82 | 0.84 | 75 | empty |
| 2 | 225 | 0.81 | 0.94 | 33 | 137 |
| 3 | 1063 | 0.81 | 0.82 | 98 | GOL |
| 4 | 177 | 0.80 | 0.95 | 32 | 137 |
| 5 | 197 | 0.80 | 0.94 | 34 | 137 |
Interfaces
14 interfaces between chains.
- A–C · 620 Ų buried · 6 hydrogen bonds · protein-protein
- E–H · 559 Ų buried · 7 hydrogen bonds · protein-protein
- D–G · 549 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 543 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 534 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6Y88 · IGPS (Indole-3-glycerol phosphate synthase) from Pseudomonas aeruginosa in complex with… · the same entry in another collection · chain B against B, 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 A0A367MAM9
- Elsewhere: RCSB PDB 6Y88 · PDBe 6Y88 · UniProt A0A367MAM9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.