MolNFT v1 · #109310 · protein
Crystal structure of scribble PDZ34 tandem in complex with its target peptide
4WYU · Protein scribble homolog: “Crystal structure of scribble PDZ34 tandem in complex with its target peptide”. X-ray diffraction, 1 ligand (IOD), 7 pockets (best druggability 0.53). MolNFT v1 #109310 on GenesisL1: 3D structure, binding…
- 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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