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Yersinia yoph (residues 163-468) binds phosphonodifluoromethyl-phe containing hexapeptide at two sites
Analyse Yersinia yoph (residues 163-468) binds phosphonodifluoromethyl-phe containing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XXV
- Type
- protein
- Length
- 584 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-tyrosine phosphatase yoph; Epidermal growth factor receptor derived peptide
- EC
- 3.1.3.48
- UniProt
- P15273
- Ligands
- NH2
- Pockets
- 7 · best druggability 0.49
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein-tyrosine phosphatase yoph (EC 3.1.3.48) | protein | 282 | 36% helix, 21% strand | P15273 |
| C, E | Epidermal growth factor receptor derived peptide | protein | 4 | 0% helix, 0% strand | — |
| D, F | Epidermal growth factor receptor derived peptide | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- NH2 · Amino group · ion · 4 copies · chains A, C, D, B, E, F
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 | 154 | 0.49 | 0.78 | 21 | empty |
| 2 | 172 | 0.47 | 0.76 | 30 | empty |
| 3 | 144 | 0.46 | 0.77 | 21 | empty |
| 4 | 182 | 0.43 | 0.74 | 30 | empty |
| 5 | 137 | 0.42 | 0.75 | 30 | empty |
Interfaces
5 interfaces between chains.
- A–D · 436 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 436 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 432 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 429 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 351 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 1XXV · Yersinia YopH (residues 163-468) binds phosphonodifluoromethyl-Phe containing hexapeptide… · the same entry in another collection · chain C against C, TM-score 1.00
- P15273 · AlphaFold monomer V2.0 prediction for tyrosine-protein phosphatase yoph (P15273) · a predicted model of the same protein · chain A 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 1XXV · PDBe 1XXV · UniProt P15273
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