Research workbench
Crystal structure of the L317I mutant of the chicken C-src tyrosine kinase domain complexed with imatinib
Analyse Crystal structure of the L317I mutant of the chicken C-src tyrosine kinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OEZ
- Type
- protein
- Length
- 522 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase src
- EC
- 2.7.10.2
- UniProt
- P00523
- Ligands
- STI
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 261 | 43% helix, 16% strand | P00523 |
| B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 261 | 40% helix, 16% strand | P00523 |
Ligands and binding sites
- STI · 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)-phenyl]-benzamide · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 646 | 0.75 | 0.81 | 71 | STI |
| 2 | 397 | 0.71 | 0.82 | 50 | STI |
| 3 | 294 | 0.59 | 0.78 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 410 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3OEZ · crystal structure of the L317I mutant of the chicken c-Src tyrosine kinase domain… · 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 P00523
- Elsewhere: RCSB PDB 3OEZ · PDBe 3OEZ · UniProt P00523
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