Research workbench
Crystal structure of the tyrosine phosphatase shp-2 with Y279C mutation
Analyse Crystal structure of the tyrosine phosphatase shp-2 with Y279C mutation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GWF
- Type
- protein
- Length
- 990 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein phosphatase non-receptor type 11
- EC
- 3.1.3.48
- UniProt
- Q06124
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) | protein | 497 | 31% helix, 25% strand | Q06124 |
| B | Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) | protein | 493 | 31% helix, 24% strand | Q06124 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
- GOL · Glycerol · additive · chains A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1080 | 0.76 | 0.78 | 97 | EDO |
| 2 | 333 | 0.62 | 0.79 | 28 | empty |
| 3 | 327 | 0.61 | 0.78 | 34 | PGE |
| 4 | 93 | 0.51 | 0.83 | 17 | empty |
| 5 | 80 | 0.44 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 633 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4GWF · Crystal structure of the tyrosine phosphatase SHP-2 with Y279C mutation · the same entry in another collection · chain A against A, TM-score 1.00
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 Q06124
- Elsewhere: RCSB PDB 4GWF · PDBe 4GWF · UniProt Q06124
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