Research workbench
Crystal structure of SHANK1 PDZ in complex with a peptide-small molecule hybrid
Analyse Crystal structure of SHANK1 PDZ in complex with a peptide-small molecule hybrid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YX1
- Type
- protein
- Length
- 216 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Homo sapiens
- Molecule
- SH3 and multiple ankyrin repeat domains protein 1
- UniProt
- Q9Y566
- Ligands
- PWT
Structure
x-ray diffraction · resolution 1.8 · 2 distinct chains · 14% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SH3 and multiple ankyrin repeat domains protein 1 | protein | 104 | 14% helix, 41% strand | Q9Y566 |
| B | SH3 and multiple ankyrin repeat domains protein 1 | protein | 112 | 13% helix, 41% strand | Q9Y566 |
Ligands and binding sites
- PWT · 2-[[2-(5-oxidanylidenepentanoyl) hydrazinyl]methyl]benzoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 1028 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6YX1 · Crystal structure of SHANK1 PDZ in complex with a peptide-small molecule hybrid · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y566 · AlphaFold monomer V2.0 prediction for SH3 and multiple ankyrin repeat domains protein 1… · a predicted model of the same protein · chain A against A, TM-score 0.91
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 Q9Y566
- Elsewhere: RCSB PDB 6YX1 · PDBe 6YX1 · UniProt Q9Y566
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