Research workbench
Crystal structure of C-src SH3 domain without atcun motif: monomer 2
Analyse Crystal structure of C-src SH3 domain without atcun motif: monomer 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XVM
- Type
- protein
- Length
- 237 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
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 59 | 5% helix, 42% strand | P00523 |
| B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 58 | 0% helix, 41% strand | P00523 |
| C, D | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 60 | 5% helix, 42% strand | P00523 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.67 | 0.79 | 66 | empty |
| 2 | 50 | 0.32 | 0.78 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–C · 372 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 318 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 304 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6XVM · Crystal structure of c-Src SH3 domain without ATCUN motif: monomer 2 · 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 6XVM · PDBe 6XVM · UniProt P00523
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