Research workbench
Crystal structure of the PTP epsilon D1 domain
Analyse Crystal structure of the PTP epsilon D1 domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D4D
- Type
- protein
- Length
- 564 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.765
- Source
- Homo sapiens
- Molecule
- Receptor-type tyrosine-protein phosphatase epsilon
- EC
- 3.1.3.48
- UniProt
- P23469
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · resolution 1.765 · 2 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-type tyrosine-protein phosphatase epsilon (EC 3.1.3.48) | protein | 283 | 37% helix, 24% strand | P23469 |
| B | Receptor-type tyrosine-protein phosphatase epsilon (EC 3.1.3.48) | protein | 281 | 37% helix, 24% strand | P23469 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.61 | 0.77 | 38 | empty |
| 2 | 258 | 0.57 | 0.78 | 39 | empty |
| 3 | 172 | 0.51 | 0.78 | 23 | empty |
| 4 | 141 | 0.45 | 0.77 | 24 | empty |
| 5 | 89 | 0.37 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 463 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6D4D · Crystal structure of the ptp epsilon D1 domain · the same entry in another collection · chain A against A, TM-score 1.00
- P23469 · AlphaFold monomer V2.0 prediction for receptor-type tyrosine-protein phosphatase epsilon… · a predicted model of the same protein · 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 P23469
- Elsewhere: RCSB PDB 6D4D · PDBe 6D4D · UniProt P23469
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