Research workbench
Crystal structure of the catalytic domain of PTP10D from drosophila melanogaster with a phosphopeptide substrate GP4
Analyse Crystal structure of the catalytic domain of PTP10D from drosophila… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S3H
- Type
- protein
- Length
- 572 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein phosphatase 10D
- EC
- 3.1.3.48
- UniProt
- P35992
- Ligands
- PTR
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein phosphatase 10D (EC 3.1.3.48) | protein | 287 | 35% helix, 20% strand | P35992 |
| B | Tyrosine-protein phosphatase 10D (EC 3.1.3.48) | protein | 285 | 33% helix, 22% strand | P35992 |
Ligands and binding sites
- PTR · O-phosphotyrosine · ligand · chains B
- 1BO · 1-butanol · additive · chains A
- BU1 · 1,4-butanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.63 | 0.77 | 51 | PTR |
| 2 | 242 | 0.55 | 0.77 | 34 | empty |
| 3 | 135 | 0.43 | 0.76 | 19 | empty |
| 4 | 109 | 0.41 | 0.76 | 21 | empty |
| 5 | 82 | 0.32 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 705 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3S3H · Crystal structure of the catalytic domain of PTP10D from Drosophila melanogaster with a… · 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 P35992
- Elsewhere: RCSB PDB 3S3H · PDBe 3S3H · UniProt P35992
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