Research workbench
NCK1 SH2-domain in complex with a dodecaphosphopeptide from epec protein tir
Analyse NCK1 SH2-domain in complex with a dodecaphosphopeptide from epec protein tir in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CI9
- Type
- protein
- Length
- 223 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytoplasmic protein NCK1; Translocated intimin receptor
- UniProt
- P16333, O50190
- Pockets
- 1 · best druggability 0.34
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytoplasmic protein NCK1 | protein | 102 | 21% helix, 32% strand | P16333 |
| B | Cytoplasmic protein NCK1 | protein | 100 | 21% helix, 35% strand | P16333 |
| L | Translocated intimin receptor | protein | 9 | 0% helix, 0% strand | O50190 |
| M | Translocated intimin receptor | protein | 12 | 0% helix, 0% strand | O50190 |
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 | 85 | 0.34 | 0.74 | 13 | empty |
Interfaces
3 interfaces between chains.
- B–M · 680 Ų buried · 21 hydrogen bonds · protein-protein
- A–L · 613 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 211 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 2CI9 · Nck1 SH2-domain in complex with a dodecaphosphopeptide from EPEC protein Tir · the same entry in another collection · chain A against A, TM-score 1.00
- P16333 · AlphaFold monomer V2.0 prediction for cytoplasmic protein NCK1 (P16333) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P16333
- Every structure of UniProt O50190
- Elsewhere: RCSB PDB 2CI9 · PDBe 2CI9 · UniProt P16333 · UniProt O50190
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