Research workbench
Crystal structure of yoph mutant D356A complexed with irreversible inhibitor pvsn
Analyse Crystal structure of yoph mutant D356A complexed with irreversible inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BM8
- Type
- protein
- Length
- 282 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein phosphatase yoph
- EC
- 3.1.3.48
- UniProt
- P15273
- Ligands
- PSY
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein phosphatase yoph (EC 3.1.3.48) | protein | 282 | 34% helix, 21% strand | P15273 |
Ligands and binding sites
- PSY · phenyl ethenesulfonate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.52 | 0.78 | 23 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3BM8 · crystal structure of YopH mutant D356A complexed with irreversible inhibitor PVSN · 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 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 3BM8 · PDBe 3BM8 · UniProt P15273
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