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Crystal structure of the N-terminal IG1-2 module of human receptor protein tyrosine phosphatase delta
Analyse Crystal structure of the N-terminal IG1-2 module of human receptor protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YD7
- Type
- protein
- Length
- 392 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ptprd protein
- EC
- 3.1.3.48
- UniProt
- Q3KPJ2
- Ligands
- PO4
- Pockets
- 5 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ptprd protein (EC 3.1.3.48) | protein | 197 | 3% helix, 58% strand | Q3KPJ2 |
| B | Ptprd protein (EC 3.1.3.48) | protein | 195 | 5% helix, 58% strand | Q3KPJ2 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.47 | 0.77 | 26 | empty |
| 2 | 122 | 0.45 | 0.77 | 20 | empty |
| 3 | 101 | 0.36 | 0.75 | 15 | empty |
| 4 | 81 | 0.30 | 0.72 | 13 | empty |
| 5 | 57 | 0.26 | 0.72 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 495 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2YD7 · Crystal structure of the N-terminal Ig1-2 module of Human Receptor Protein Tyrosine… · 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 Q3KPJ2
- Elsewhere: RCSB PDB 2YD7 · PDBe 2YD7 · UniProt Q3KPJ2
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