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Crystal structure of a Low Molecular Weight Phosphotyrosine phosphatase from Vibrio choleraeO395
Analyse Crystal structure of a Low Molecular Weight Phosphotyrosine phosphatase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LRQ
- Type
- protein
- Length
- 595 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.45
- Source
- Vibrio cholerae
- Molecule
- Phosphotyrosine protein phosphatase
- EC
- 3.1.3.48
- UniProt
- A5F2Q3
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · resolution 1.45 · 4 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphotyrosine protein phosphatase (EC 3.1.3.48) | protein | 148 | 47% helix, 14% strand | A5F2Q3 |
| B | Phosphotyrosine protein phosphatase (EC 3.1.3.48) | protein | 150 | 48% helix, 15% strand | A5F2Q3 |
| C | Phosphotyrosine protein phosphatase (EC 3.1.3.48) | protein | 149 | 45% helix, 15% strand | A5F2Q3 |
| D | Phosphotyrosine protein phosphatase (EC 3.1.3.48) | protein | 148 | 47% helix, 15% strand | A5F2Q3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, C, B, D
- MPO · 3[N-morpholino]propane sulfonic acid · additive · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 949 | 0.77 | 0.80 | 76 | SO4 |
| 2 | 306 | 0.73 | 0.85 | 43 | MPO |
| 3 | 301 | 0.73 | 0.85 | 36 | MPO |
| 4 | 99 | 0.37 | 0.75 | 21 | empty |
| 5 | 77 | 0.32 | 0.74 | 13 | empty |
Interfaces
5 interfaces between chains.
- B–D · 531 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 512 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 291 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 263 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 217 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4LRQ · Crystal structure of a low molecular weight phosphotyrosine phosphatase from vibrio… · 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 A5F2Q3
- Elsewhere: RCSB PDB 4LRQ · PDBe 4LRQ · UniProt A5F2Q3
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