MolNFT v1 · #47827 · protein
Crystal structure of human protein tyrosine phosphatase PTPN9
2PA5 · Tyrosine-protein phosphatase non-receptor type 9: “Crystal structure of human protein tyrosine phosphatase PTPN9”. X-ray diffraction, 2 ligands (CL, SCN), 5 pockets (best druggability 0.77). MolNFT v1 #47827 on GenesisL1: 3D…
- PDB
- 2PA5
- Type
- protein
- Length
- 587 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein phosphatase non-receptor type 9
- EC
- 3.1.3.48
- UniProt
- P43378
- Ligands
- CL, SCN
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein phosphatase non-receptor type 9 (EC 3.1.3.48) | protein | 296 | 37% helix, 24% strand | P43378 |
| B | Tyrosine-protein phosphatase non-receptor type 9 (EC 3.1.3.48) | protein | 291 | 37% helix, 24% strand | P43378 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B
- SCN · Thiocyanate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 5 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.77 | 0.79 | 87 | SCN, EDO |
| 2 | 120 | 0.51 | 0.81 | 17 | EDO |
| 3 | 155 | 0.47 | 0.76 | 25 | CL |
| 4 | 103 | 0.42 | 0.78 | 19 | empty |
| 5 | 132 | 0.40 | 0.74 | 23 | EDO |
Interfaces
1 interface between chains.
- A–B · 892 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2PA5 · Crystal structure of human protein tyrosine phosphatase PTPN9 · the same entry in another collection · chain A against A, TM-score 1.00
- P43378 · AlphaFold monomer V2.0 prediction for tyrosine-protein phosphatase non-receptor type 9… · 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 P43378
- Elsewhere: RCSB PDB 2PA5 · PDBe 2PA5 · UniProt P43378
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