MolNFT v1 · #171209 · protein
Crystal structure of SHANK1 PDZ in complex with a peptide-small molecule hybrid
6YWZ · SH3 and multiple ankyrin repeat domains protein 1: “Crystal structure of SHANK1 PDZ in complex with a peptide-small molecule hybrid”. X-ray diffraction, 1 ligand (PWN), 1 pocket (best druggability 0.67). MolNFT v1 #171209 on…
- PDB
- 6YWZ
- Type
- protein
- Length
- 217 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SH3 and multiple ankyrin repeat domains protein 1
- UniProt
- Q9Y566
- Ligands
- PWN
- Pockets
- 1 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | SH3 and multiple ankyrin repeat domains protein 1 | protein | 112 | 13% helix, 39% strand | Q9Y566 |
| A | SH3 and multiple ankyrin repeat domains protein 1 | protein | 105 | 14% helix, 39% strand | Q9Y566 |
Ligands and binding sites
- PWN · 2-[(~{E})-(4-oxidanylidenebutanoylhydrazinylidene) methyl]benzoic acid · ligand · 2 copies · chains B, A
- PEG · Di(hydroxyethyl)ether · additive · chains B
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 | 92 | 0.67 | 0.91 | 29 | empty |
Interfaces
1 interface between chains.
- B–A · 905 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6YWZ · Crystal structure of SHANK1 PDZ in complex with a peptide-small molecule hybrid · the same entry in another collection · chain B against B, 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 0.90
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 6YWZ · PDBe 6YWZ · UniProt Q9Y566
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