MolNFT v1 · #78250 · protein
Crystal structure of the catalytic domain of PTP10D from drosophila melanogaster with a small molecule inhibitor vanadate
3S3F · Tyrosine-protein phosphatase 10D: “Crystal structure of the catalytic domain of PTP10D from drosophila melanogaster with a small molecule…”. X-ray diffraction, 1 ligand (VO4), 4 pockets (best druggability 0.68). MolNFT v1 #78250 on…
- PDB
- 3S3F
- 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
- VO4
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein phosphatase 10D (EC 3.1.3.48) | protein | 287 | 34% helix, 20% strand | P35992 |
| B | Tyrosine-protein phosphatase 10D (EC 3.1.3.48) | protein | 285 | 35% helix, 22% strand | P35992 |
Ligands and binding sites
- VO4 · Vanadate ion · ion · chains B
- 1BO · 1-butanol · additive · 2 copies · chains A, B
- IPA · Isopropyl alcohol · additive · 2 copies · chains A
- BU1 · 1,4-butanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 644 | 0.68 | 0.77 | 64 | VO4 |
| 2 | 206 | 0.53 | 0.78 | 27 | empty |
| 3 | 145 | 0.43 | 0.75 | 25 | empty |
| 4 | 101 | 0.34 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 676 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3S3F · 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 3S3F · PDBe 3S3F · UniProt P35992
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