Research workbench
Crystal structure of the src SH2 domain complexed with peptide (sdpyanfk)
Analyse Crystal structure of the src SH2 domain complexed with peptide (sdpyanfk) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1P13
- Type
- protein
- Length
- 218 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase src; Peptide
- EC
- 2.7.1.112
- UniProt
- P00523
- Pockets
- 1 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.1.112) | protein | 102 | 18% helix, 33% strand | P00523 |
| C, D | Peptide | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- CAC · Cacodylate ion · additive · 4 copies · chains A, D, B, C
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 | 123 | 0.42 | 0.76 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–D · 483 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 478 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 321 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 covalent (phosphorylation, additive adduct).
Compared structures
- 1P13 · Crystal Structure of the Src SH2 Domain Complexed with Peptide (SDpYANFK) · 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 1P13 · PDBe 1P13 · UniProt P00523
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