Research workbench
Crystal structure of YOPHQ357F(CATALYTIC domain, residues 163-468) in complex with pncs
Analyse Crystal structure of YOPHQ357F(CATALYTIC domain, residues 163-468) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U96
- Type
- protein
- Length
- 564 residues
- Chains
- 2
- 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
- CSN, SO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tyrosine-protein phosphatase yoph (EC 3.1.3.48) | protein | 282 | 39% helix, 21% strand | P15273 |
Ligands and binding sites
- CSN · N,4-dihydroxy-N-oxo-3-(sulfooxy)benzenaminium · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.78 | 0.81 | 74 | empty |
| 2 | 111 | 0.62 | 0.88 | 27 | empty |
| 3 | 253 | 0.56 | 0.78 | 27 | empty |
| 4 | 51 | 0.44 | 0.84 | 15 | CSN |
| 5 | 113 | 0.44 | 0.78 | 23 | CSN |
Interfaces
1 interface between chains.
- A–B · 969 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3U96 · Crystal Structure of YopHQ357F(Catalytic Domain, Residues 163-468) in complex with pNCS · 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 0.98
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 P15273
- Elsewhere: RCSB PDB 3U96 · PDBe 3U96 · UniProt P15273
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