MolNFT v1 · #27902 · protein
Yersinia yoph (residues 163-468) C403S binds phosphotyrosyl peptide at two sites
1XXP · Protein-tyrosine phosphatase yoph: “Yersinia yoph (residues 163-468) C403S binds phosphotyrosyl peptide at two sites”. X-ray diffraction, 2 ligands (PTR, NH2), 7 pockets (best druggability 0.50). MolNFT v1 #27902 on GenesisL1: 3D…
- PDB
- 1XXP
- Type
- protein
- Length
- 580 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-tyrosine phosphatase yoph; Hexapeptide asp-ala-asp-glu-ptr-cle
- EC
- 3.1.3.48
- UniProt
- P15273
- Ligands
- PTR, NH2
- Pockets
- 7 · best druggability 0.50
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein-tyrosine phosphatase yoph (EC 3.1.3.48) | protein | 287 | 33% helix, 18% strand | P15273 |
| B | Protein-tyrosine phosphatase yoph (EC 3.1.3.48) | protein | 283 | 33% helix, 18% strand | P15273 |
| C, E | Hexapeptide asp-ala-asp-glu-ptr-cle | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- PTR · O-phosphotyrosine · ligand · 2 copies · chains A, B
- NH2 · Amino group · ion · 2 copies · chains C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 166 | 0.50 | 0.78 | 21 | empty |
| 2 | 163 | 0.50 | 0.78 | 22 | empty |
| 3 | 128 | 0.43 | 0.76 | 31 | empty |
| 4 | 153 | 0.41 | 0.74 | 29 | empty |
| 5 | 99 | 0.40 | 0.77 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–E · 446 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 445 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 323 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 1XXP · Yersinia YopH (residues 163-468) C403S binds phosphotyrosyl peptide at two sites · the same entry in another collection · chain A against A, TM-score 1.00
- P15273 · AlphaFold monomer V2.0 prediction for tyrosine-protein phosphatase yoph (P15273) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P15273
- Elsewhere: RCSB PDB 1XXP · PDBe 1XXP · UniProt P15273
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