Research workbench
Crystal structure of scribble PDZ34 tandem in complex with its target peptide
Analyse Crystal structure of scribble PDZ34 tandem in complex with its target peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WYU
- Type
- protein
- Length
- 416 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein scribble homolog; Peptide ser-TRP-phe-gln-thr-asp-leu
- UniProt
- Q14160
- Ligands
- IOD
- Pockets
- 7 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein scribble homolog | protein | 201 | 14% helix, 31% strand | Q14160 |
| D, C | Peptide ser-TRP-phe-gln-thr-asp-leu | protein | 7 | 0% helix, 43% strand | — |
Ligands and binding sites
- IOD · Iodide ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.53 | 0.85 | 28 | empty |
| 2 | 60 | 0.50 | 0.86 | 20 | empty |
| 3 | 66 | 0.48 | 0.84 | 22 | empty |
| 4 | 50 | 0.46 | 0.85 | 17 | empty |
| 5 | 140 | 0.44 | 0.76 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 706 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 551 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 545 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- Q14160 · AlphaFold monomer V2.0 prediction for protein scribble homolog (Q14160) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q14160
- Elsewhere: RCSB PDB 4WYU · PDBe 4WYU · UniProt Q14160
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