MolNFT v1 · #16471 · protein
Crystal structure of src SH2 domain bound to doubly phosphorylated peptide pqpyipyvpa
1NZV · Tyrosine-protein kinase transforming protein src: “Crystal structure of src SH2 domain bound to doubly phosphorylated peptide pqpyipyvpa”. X-ray diffraction, 1 ligand (CL), 1 pocket (best druggability 0.40). MolNFT v1 #16471 on…
- PDB
- 1NZV
- 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 pqpyipyvpa
- EC
- 2.7.1.112
- UniProt
- P00524
- Ligands
- CL
- Pockets
- 1 · best druggability 0.40
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 33% 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, 34% 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 pqpyipyvpa | 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 | 135 | 0.40 | 0.74 | 19 | empty |
Interfaces
2 interfaces between chains.
- B–C · 530 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 179 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 1NZV · Crystal Structure of Src SH2 domain bound to doubly phosphorylated peptide PQpYIpYVPA · 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 1NZV · PDBe 1NZV · UniProt P00524
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