Research workbench
Crystal structure of the complex between the gap domain of the pseudomonas aeruginosa exos toxin and human rac
Analyse Crystal structure of the complex between the gap domain of the pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HE1
- Type
- protein
- Length
- 622 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exoenzyme S; RAS-related C3 botulinum toxin substrate 1
- UniProt
- Q51451, P15154
- Ligands
- GDP, AF3, NI, MG
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Exoenzyme S | protein | 135 | 78% helix, 3% strand | Q51451 |
| C, D | RAS-related C3 botulinum toxin substrate 1 | protein | 176 | 39% helix, 26% strand | P15154 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, C, B, D
- AF3 · Aluminum fluoride · ligand · 2 copies · chains A, C, B, D
- NI · Nickel (II) ion · metal · 4 copies · chains A, C, D
- MG · Magnesium ion · metal · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 806 | 0.75 | 0.79 | 84 | GDP, AF3, MG |
| 2 | 897 | 0.74 | 0.78 | 76 | NI |
| 3 | 679 | 0.73 | 0.79 | 74 | GDP, AF3, MG |
| 4 | 240 | 0.53 | 0.76 | 19 | empty |
| 5 | 52 | 0.29 | 0.75 | 13 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1113 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1110 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 252 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 227 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 140 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1HE1 · Crystal structure of the complex between the GAP domain of the Pseudomonas aeruginosa… · the same entry in another collection · chain A 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 Q51451
- Every structure of UniProt P15154
- Elsewhere: RCSB PDB 1HE1 · PDBe 1HE1 · UniProt Q51451 · UniProt P15154
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