Research workbench
Crystal structure of low molecular weight phosphotyrosine phosphatase (vclmwptp-2) from vibrio CHOLERAEO395
Analyse Crystal structure of low molecular weight phosphotyrosine phosphatase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z3M
- Type
- protein
- Length
- 305 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphotyrosine protein phosphatase
- EC
- 3.1.3.48
- UniProt
- A0A0H3AM12
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphotyrosine protein phosphatase (EC 3.1.3.48) | protein | 153 | 43% helix, 12% strand | A0A0H3AM12 |
| B | Phosphotyrosine protein phosphatase (EC 3.1.3.48) | protein | 152 | 41% helix, 14% strand | A0A0H3AM12 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 35 copies · chains A, B
- MPO · 3[N-morpholino]propane sulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.38 | 0.74 | 20 | empty |
| 2 | 87 | 0.37 | 0.76 | 14 | empty |
| 3 | 66 | 0.31 | 0.75 | 13 | GOL |
Interfaces
1 interface between chains.
- A–B · 683 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5Z3M · Crystal structure of Low Molecular Weight Phosphotyrosine phosphatase (VcLMWPTP-2) from… · 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 A0A0H3AM12
- Elsewhere: RCSB PDB 5Z3M · PDBe 5Z3M · UniProt A0A0H3AM12
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