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Crystal structure of the C-src-SH3 domain E93V/Q128R mutant in complex with the high affinity peptide APP12
Analyse Crystal structure of the C-src-SH3 domain E93V/Q128R mutant in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RTW
- Type
- protein
- Length
- 142 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase src; APP12 peptide
- EC
- 2.7.10.2
- UniProt
- P00523
- Ligands
- ACE, SO4
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 5 distinct chains · 4% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 57 | 5% helix, 51% strand | P00523 |
| B | APP12 peptide | protein | 7 | 0% helix, 0% strand | — |
| C | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 57 | 5% helix, 46% strand | P00523 |
| D | APP12 peptide | protein | 12 | 0% helix, 0% strand | — |
| E | APP12 peptide | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, D, E
- GOL · Glycerol · additive · chains C, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.52 | 0.82 | 24 | SO4 |
Interfaces
8 interfaces between chains.
- A–C · 590 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 557 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 426 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 178 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 129 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4RTW · Crystal structure of the c-Src-SH3 domain E93V/Q128R mutant in complex with the high… · 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 4RTW · PDBe 4RTW · UniProt P00523
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