Research workbench
Crystal structure of PTPN3 (PTPH1) D811E mutant in complex with metavanadate
Analyse Crystal structure of PTPN3 (PTPH1) D811E mutant in complex with metavanadate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RI5
- Type
- protein
- Length
- 568 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein phosphatase non-receptor type 3
- EC
- 3.1.3.48
- UniProt
- P26045
- Ligands
- VN4
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tyrosine-protein phosphatase non-receptor type 3 (EC 3.1.3.48) | protein | 284 | 37% helix, 24% strand | P26045 |
Ligands and binding sites
- VN4 · oxido(dioxo)vanadium · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.74 | 0.79 | 84 | GOL, VN4 |
| 2 | 152 | 0.49 | 0.77 | 19 | empty |
| 3 | 103 | 0.42 | 0.77 | 18 | empty |
| 4 | 50 | 0.40 | 0.82 | 14 | empty |
| 5 | 53 | 0.27 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 466 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4RI5 · Crystal structure of PTPN3 (PTPH1) D811E mutant in complex with metavanadate · the same entry in another collection · chain B against B, TM-score 1.00
- P26045 · AlphaFold monomer V2.0 prediction for tyrosine-protein phosphatase non-receptor type 3… · 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 P26045
- Elsewhere: RCSB PDB 4RI5 · PDBe 4RI5 · UniProt P26045
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