Research workbench
Crystal structure of human protein tyrosine phosphatase PTPN9 (MEG2) complex with compound 7
Analyse Crystal structure of human protein tyrosine phosphatase PTPN9 (MEG2) complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GE6
- Type
- protein
- Length
- 607 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
- B26
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein phosphatase non-receptor type 9 (EC 3.1.3.48) | protein | 303 | 36% helix, 21% strand | P43378 |
| B | Tyrosine-protein phosphatase non-receptor type 9 (EC 3.1.3.48) | protein | 304 | 34% helix, 21% strand | P43378 |
Ligands and binding sites
- B26 · N-(4-bromo-3-methylbenzoyl)-4-[difluoro(phosphono)methyl]-L-phenylalanyl-N~5~-(3-iodobenzoyl)-L-ornithyl-3-{[(4-hydroxy-3-methoxyphenyl)acetyl]amino}-D-alaninamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.82 | 0.84 | 75 | empty |
| 2 | 150 | 0.52 | 0.80 | 24 | empty |
| 3 | 139 | 0.51 | 0.80 | 18 | empty |
| 4 | 144 | 0.46 | 0.77 | 19 | empty |
| 5 | 118 | 0.45 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 924 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4GE6 · Crystal structure of human protein tyrosine phosphatase PTPN9 (MEG2) complex with… · 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 0.99
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 4GE6 · PDBe 4GE6 · UniProt P43378
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