Research workbench
Crystal structure of the salmonella tyrosine phosphatase and GTPase activating protein sptp bound to RAC1
Analyse Crystal structure of the salmonella tyrosine phosphatase and GTPase activating… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1G4U
- Type
- protein
- Length
- 540 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein tyrosine phosphatase sptp; RAS-related C3 botulinum toxin substrate 1
- UniProt
- P74873, P63000
- Ligands
- GDP, AF3, MG
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| S | Protein tyrosine phosphatase sptp | protein | 360 | 46% helix, 17% strand | P74873 |
| R | RAS-related C3 botulinum toxin substrate 1 | protein | 180 | 39% helix, 24% strand | P63000 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains S, R
- AF3 · Aluminum fluoride · ligand · chains S, R
- MG · Magnesium ion · metal · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 659 | 0.75 | 0.81 | 79 | MG, GDP, AF3 |
| 2 | 255 | 0.56 | 0.77 | 28 | empty |
| 3 | 102 | 0.46 | 0.80 | 16 | empty |
| 4 | 134 | 0.41 | 0.75 | 17 | empty |
| 5 | 61 | 0.41 | 0.81 | 17 | empty |
Interfaces
1 interface between chains.
- S–R · 1041 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1G4U · Crystal structure of the salmonella tyrosine phosphatase and GTPase activating protein… · the same entry in another collection · chain S against S, TM-score 1.00
- P74873 · AlphaFold monomer V2.0 prediction for secreted effector protein sptp (P74873) · a predicted model of the same protein · chain S against A, TM-score 0.98
- P63000 · AlphaFold monomer V2.0 prediction for RAS-related C3 botulinum toxin substrate 1 (P63000) · a predicted model of the same protein · chain R against A, TM-score 0.98
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 P74873
- Every structure of UniProt P63000
- Elsewhere: RCSB PDB 1G4U · PDBe 1G4U · UniProt P74873 · UniProt P63000
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