Research workbench
Crystal structure of the tandem phosphatase domains of rptp CD45 with a ptyr peptide
Analyse Crystal structure of the tandem phosphatase domains of rptp CD45 with a ptyr… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YGU
- Type
- protein
- Length
- 1,161 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leukocyte common antigen; Polyoma middle T antigen
- EC
- 3.1.3.48
- UniProt
- P08575, P03077
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leukocyte common antigen (EC 3.1.3.48) | protein | 571 | 31% helix, 20% strand | P08575 |
| B | Leukocyte common antigen (EC 3.1.3.48) | protein | 582 | 31% helix, 20% strand | P08575 |
| C, D | Polyoma middle T antigen | protein | 4 | 0% helix, 0% strand | P03077 |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.80 | 0.81 | 99 | empty |
| 2 | 392 | 0.80 | 0.89 | 34 | empty |
| 3 | 113 | 0.69 | 0.91 | 18 | empty |
| 4 | 109 | 0.37 | 0.74 | 16 | empty |
| 5 | 53 | 0.30 | 0.76 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–C · 396 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 391 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 54 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered, phosphorylation).
Compared structures
- 1YGU · Crystal structure of the tandem phosphatase domains of RPTP CD45 with a pTyr peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P08575 · AlphaFold monomer V2.0 prediction for receptor-type tyrosine-protein phosphatase C… · a predicted model of the same protein · chain A 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 P08575
- Every structure of UniProt P03077
- Elsewhere: RCSB PDB 1YGU · PDBe 1YGU · UniProt P08575 · UniProt P03077
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