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
- 6YX2
- Type
- protein
- Length
- 220 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SH3 and multiple ankyrin repeat domains protein 1; Pww-thr-arg-leu
- UniProt
- Q9Y566
- Ligands
- PWW
- Pockets
- 1 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SH3 and multiple ankyrin repeat domains protein 1 | protein | 103 | 15% helix, 40% strand | Q9Y566 |
| B | SH3 and multiple ankyrin repeat domains protein 1 | protein | 111 | 14% helix, 39% strand | Q9Y566 |
| C, D | Pww-thr-arg-leu | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- PWW · 4-[[(~{E})-5-oxidanylidenepentanoyldiazenyl]methyl]benzoic acid · ligand · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.68 | 0.89 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 904 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 340 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 335 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6YX2 · 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 0.93
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 6YX2 · PDBe 6YX2 · UniProt Q9Y566
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