MolNFT v1 · #7376 · protein
Crystal structure of the salmonella tyrosine phosphatase and GTPase activating protein sptp bound to RAC1
1G4U · Protein tyrosine phosphatase sptp: “Crystal structure of the salmonella tyrosine phosphatase and GTPase activating protein sptp bound to RAC1”. X-ray diffraction, 3 ligands (GDP, AF3, MG), 6 pockets (best druggability 0.75). MolNFT…
- 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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