Research workbench
Crystal structure of human nck SH3.1 in complex with peptide pppvpnpdy
Analyse Crystal structure of human nck SH3.1 in complex with peptide pppvpnpdy in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5QU2
- Type
- protein
- Length
- 130 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytoplasmic protein NCK1; ACE-pro-pro-pro-val-pro-asn-pro-asp-tyr-NH2
- UniProt
- P16333
- Ligands
- ACE, SO4, NH2
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytoplasmic protein NCK1 | protein | 56 | 5% helix, 46% strand | P16333 |
| B | Cytoplasmic protein NCK1 | protein | 56 | 5% helix, 45% strand | P16333 |
| D, E | ACE-pro-pro-pro-val-pro-asn-pro-asp-tyr-NH2 | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains D, B, E
- SO4 · Sulfate ion · ion · 3 copies · chains A, D
- NH2 · Amino group · ion · 2 copies · chains D, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
4 interfaces between chains.
- A–D · 505 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 495 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 471 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 90 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5QU2 · Crystal Structure of human Nck SH3.1 in complex with peptide PPPVPNPDY · 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 A against A, TM-score 0.98
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
- Elsewhere: RCSB PDB 5QU2 · PDBe 5QU2 · UniProt P16333
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