Research workbench
Crystal structure of SHANK1 PDZ domain with ARAP3-derived peptide
Analyse Crystal structure of SHANK1 PDZ domain with ARAP3-derived peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A9B
- Type
- protein
- Length
- 253 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SH3 and multiple ankyrin repeat domains protein 1,ARF-gap with rho-gap domain, ank repeat…
- UniProt
- Q9WV48, Q8WWN8
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SH3 and multiple ankyrin repeat domains protein 1,ARF-gap with rho-gap domain, ank repeat and pH domain-containing protein 3 | protein | 121 | 16% helix, 38% strand | Q9WV48, Q8WWN8 |
| B | SH3 and multiple ankyrin repeat domains protein 1,ARF-gap with rho-gap domain, ank repeat and pH domain-containing protein 3 | protein | 132 | 11% helix, 42% strand | Q9WV48, Q8WWN8 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 590 | 0.77 | 0.83 | 55 | EDO |
| 2 | 73 | 0.48 | 0.83 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1990 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 7A9B · Crystal structure of Shank1 PDZ domain with ARAP3-derived peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WV48 · 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 0.88
- Q8WWN8 · AlphaFold monomer V2.0 prediction for arf-gap with rho-gap domain, ank repeat and pH… · a predicted model of the same protein · chain A against A, TM-score 0.37
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 Q9WV48
- Every structure of UniProt Q8WWN8
- Elsewhere: RCSB PDB 7A9B · PDBe 7A9B · UniProt Q9WV48 · UniProt Q8WWN8
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