Research workbench
Crystal structure of a yeast low molecular weight protein tyrosine phosphatase (LTP1) complexed with the substrate pnpp
Analyse Crystal structure of a yeast low molecular weight protein tyrosine phosphatase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D1Q
- Type
- protein
- Length
- 317 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine phosphatase (E.C.3.1.3.48)
- EC
- 3.1.3.48
- UniProt
- P40347
- Ligands
- 4NP, PO4
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine phosphatase (E.C.3.1.3.48) (EC 3.1.3.48) | protein | 159 | 43% helix, 16% strand | P40347 |
| B | Tyrosine phosphatase (E.C.3.1.3.48) (EC 3.1.3.48) | protein | 158 | 42% helix, 15% strand | P40347 |
Ligands and binding sites
- 4NP · 4-nitrophenyl phosphate · ligand · chains A
- PO4 · Phosphate ion · ion · chains B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 474 | 0.64 | 0.77 | 40 | empty |
| 2 | 55 | 0.39 | 0.80 | 13 | 4NP |
Interfaces
1 interface between chains.
- A–B · 349 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1D1Q · Crystal structure of a yeast low molecular weight protein tyrosine phosphatase (LTP1)… · the same entry in another collection · chain A against A, TM-score 1.00
- P40347 · AlphaFold monomer V2.0 prediction for low molecular weight phosphotyrosine protein… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P40347
- Elsewhere: RCSB PDB 1D1Q · PDBe 1D1Q · UniProt P40347
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