Research workbench
C-src kinase domain THR338ILE mutant in complex with atpgs
Analyse C-src kinase domain THR338ILE mutant in complex with atpgs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DQW
- Type
- protein
- Length
- 1,111 residues
- Chains
- 4
- 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
- AGS, MG
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 279 | 41% helix, 19% strand | P00523 |
| C | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 276 | 42% helix, 18% strand | P00523 |
| D | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 277 | 40% helix, 18% strand | P00523 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium 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
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.78 | 0.80 | 69 | AGS, MG |
| 2 | 1189 | 0.78 | 0.80 | 98 | AGS, MG |
| 3 | 467 | 0.66 | 0.78 | 49 | AGS, MG |
| 4 | 410 | 0.66 | 0.79 | 38 | AGS, MG |
| 5 | 64 | 0.61 | 0.91 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 775 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 688 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 678 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 110 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 106 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 3DQW · c-Src kinase domain Thr338Ile mutant in complex with ATPgS · 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 3DQW · PDBe 3DQW · UniProt P00523
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