Research workbench
Crystal structure of the fyn SH3 domain in space group P1 at pH 7.5
Analyse Crystal structure of the fyn SH3 domain in space group P1 at pH 7.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A2K
- Type
- protein
- Length
- 233 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase fyn
- EC
- 2.7.10.2
- UniProt
- P06241
- Ligands
- NA
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tyrosine-protein kinase fyn (EC 2.7.10.2) | protein | 58 | 5% helix, 45% strand | P06241 |
| C | Tyrosine-protein kinase fyn (EC 2.7.10.2) | protein | 58 | 5% helix, 41% strand | P06241 |
| D | Tyrosine-protein kinase fyn (EC 2.7.10.2) | protein | 59 | 5% helix, 41% strand | P06241 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.41 | 0.75 | 25 | empty |
| 2 | 116 | 0.39 | 0.75 | 23 | empty |
| 3 | 59 | 0.28 | 0.74 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–C · 410 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 403 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 360 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 324 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 218 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7A2K · Crystal structure of the Fyn SH3 domain in space group P1 at pH 7.5 · the same entry in another collection · chain D against D, TM-score 1.00
- P06241 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase fyn (P06241) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P06241
- Elsewhere: RCSB PDB 7A2K · PDBe 7A2K · UniProt P06241
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