MolNFT v1 · #171210 · protein
Crystal structure of SHANK1 PDZ in complex with a peptide-small molecule hybrid
6YX0 · 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 (PWQ), 1 pocket (best druggability 0.68). MolNFT v1 #171210 on…
- PDB
- 6YX0
- Type
- protein
- Length
- 219 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SH3 and multiple ankyrin repeat domains protein 1; Pwq-thr-arg-leu
- UniProt
- Q9Y566
- Ligands
- PWQ
- Pockets
- 1 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SH3 and multiple ankyrin repeat domains protein 1 | protein | 101 | 15% helix, 42% strand | Q9Y566 |
| B | SH3 and multiple ankyrin repeat domains protein 1 | protein | 112 | 13% helix, 38% strand | Q9Y566 |
| C, D | Pwq-thr-arg-leu | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- PWQ · 4-[[2-(4-oxidanylidenebutanoyl) hydrazinyl]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 | 148 | 0.68 | 0.88 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–B · 842 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 333 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 325 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6YX0 · 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 0.94
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 6YX0 · PDBe 6YX0 · UniProt Q9Y566
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