MolNFT v1 · #172439 · protein
Crystal structure of the fyn SH3 domain in space group P1 at pH 7.5
7A2K · Tyrosine-protein kinase fyn: “Crystal structure of the fyn SH3 domain in space group P1 at pH 7.5”. X-ray diffraction, 1 ligand (NA), 3 pockets (best druggability 0.41). MolNFT v1 #172439 on GenesisL1: 3D structure, binding sites…
- 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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