Research workbench
Crystal structure of src SH2 domain bound to doubly phosphorylated peptide pqpyepyipi
Analyse Crystal structure of src SH2 domain bound to doubly phosphorylated peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NZL
- Type
- protein
- Length
- 212 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase transforming protein src; Doubly phosphorylated peptide ligand…
- EC
- 2.7.1.112
- UniProt
- P00524
- Ligands
- CL
- Pockets
- 1 · best druggability 0.40
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase transforming protein src (EC 2.7.1.112) | protein | 101 | 16% helix, 32% strand | P00524 |
| B | Tyrosine-protein kinase transforming protein src (EC 2.7.1.112) | protein | 103 | 17% helix, 35% strand | P00524 |
| C | Doubly phosphorylated peptide ligand (pqpyepyipi) | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
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 | 131 | 0.40 | 0.74 | 18 | empty |
Interfaces
2 interfaces between chains.
- B–C · 547 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 173 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 1NZL · Crystal Structure of Src SH2 domain bound to doubly phosphorylated peptide PQpYEpYIPI · 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 P00524
- Elsewhere: RCSB PDB 1NZL · PDBe 1NZL · UniProt P00524
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