Research workbench
C-src (SH2 domain) complexed with ACE-formyl phosphotyr-glu-(N,N- dipentyl amine)
Analyse C-src (SH2 domain) complexed with ACE-formyl phosphotyr-glu-(N,N- dipentyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1A09
- Type
- protein
- Length
- 212 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-src tyrosine kinase; ACE-formyl phosphotyr-glu-(N,N-dipentyl amine)
- EC
- 2.7.1.112
- UniProt
- P12931
- Ligands
- ACE, DIP
- Pockets
- 1 · best druggability 0.45
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C-src tyrosine kinase (EC 2.7.1.112) | protein | 106 | 21% helix, 32% strand | P12931 |
| C, D | ACE-formyl phosphotyr-glu-(N,N-dipentyl amine) | protein | 2 | 0% helix, 0% strand | — |
| B | C-src tyrosine kinase (EC 2.7.1.112) | protein | 102 | 19% helix, 29% strand | P12931 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, C, B, D
- DIP · Dipentylamine · ligand · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.45 | 0.75 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–B · 465 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 314 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 312 Ų buried · 9 hydrogen bonds · protein-protein
- C–B · 75 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 1A09 · C-src (SH2 domain) complexed with ace-formyl phosphotyr-glu-(n,n-dipentyl amine) · the same entry in another collection · chain A against A, TM-score 1.00
- P12931 · AlphaFold monomer V2.0 prediction for proto-oncogene tyrosine-protein kinase src (P12931) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P12931
- Elsewhere: RCSB PDB 1A09 · PDBe 1A09 · UniProt P12931
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