Research workbench
Crystal structure of the Src homology-2 domain of SH2-B in complex with Jak2 pTyr813 phosphopeptide
Analyse Crystal structure of the Src homology-2 domain of SH2-B in complex with Jak2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HDX
- Type
- protein
- Length
- 684 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.35
- Source
- Mus musculus; SYNTHETIC CONSTRUCT
- Molecule
- SH2-B PH domain containing signaling mediator 1 gamma isoform; Jak2 protein
- UniProt
- Q9WVM5, Q7TQD0
- Pockets
- 9 · best druggability 0.56
Structure
x-ray diffraction · resolution 2.35 · 5 distinct chains · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | SH2-B PH domain containing signaling mediator 1 gamma isoform | protein | 108 | 23% helix, 31% strand | Q9WVM5 |
| B, D | SH2-B PH domain containing signaling mediator 1 gamma isoform | protein | 105 | 25% helix, 30% strand | Q9WVM5 |
| F | SH2-B PH domain containing signaling mediator 1 gamma isoform | protein | 104 | 25% helix, 32% strand | Q9WVM5 |
| G, L | Jak2 protein | protein | 9 | 0% helix, 11% strand | Q7TQD0 |
| H, I, J, K | Jak2 protein | protein | 7 | 0% helix, 14% strand | Q7TQD0 |
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 189 | 0.56 | 0.80 | 26 | empty |
| 2 | 179 | 0.54 | 0.79 | 30 | empty |
| 3 | 214 | 0.53 | 0.77 | 28 | empty |
| 4 | 187 | 0.52 | 0.78 | 30 | empty |
| 5 | 182 | 0.51 | 0.77 | 28 | empty |
Interfaces
14 interfaces between chains.
- F–L · 727 Ų buried · 16 hydrogen bonds · protein-protein
- A–G · 725 Ų buried · 14 hydrogen bonds · protein-protein
- E–K · 683 Ų buried · 13 hydrogen bonds · protein-protein
- D–J · 682 Ų buried · 13 hydrogen bonds · protein-protein
- C–I · 670 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (phosphorylation).
Compared structures
- 2HDX · Crystal structure of the src homology-2 domain of SH2-B in complex with JAK2 PTYR813… · 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 Q9WVM5
- Every structure of UniProt Q7TQD0
- Elsewhere: RCSB PDB 2HDX · PDBe 2HDX · UniProt Q9WVM5 · UniProt Q7TQD0
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