Research workbench
Crystal structure of human scribble PDZ3:VANGL2 complex
Analyse Crystal structure of human scribble PDZ3:VANGL2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XA6
- Type
- protein
- Length
- 180 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein scribble homolog; Vang-like protein 2
- UniProt
- Q14160, Q9ULK5
- Pockets
- 1 · best druggability 0.35
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Protein scribble homolog | protein | 84 | 15% helix, 40% strand | Q14160 |
| C | Vang-like protein 2 | protein | 6 | 0% helix, 50% strand | Q9ULK5 |
| A | Protein scribble homolog | protein | 83 | 16% helix, 41% strand | Q14160 |
| D | Vang-like protein 2 | protein | 7 | 0% helix, 43% strand | Q9ULK5 |
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
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.35 | 0.77 | 23 | empty |
Interfaces
6 interfaces between chains.
- B–C · 453 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 440 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 217 Ų buried · 4 hydrogen bonds · protein-protein
- B–A · 132 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 127 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6XA6 · Crystal Structure of Human Scribble PDZ3:Vangl2 Complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q14160 · AlphaFold monomer V2.0 prediction for protein scribble homolog (Q14160) · a predicted model of the same protein · chain B against A, TM-score 0.96
- Q9ULK5 · AlphaFold monomer V2.0 prediction for vang-like protein 2 (Q9ULK5) · a predicted model of the same protein · chain C against A, TM-score 0.80
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
- Every structure of UniProt Q9ULK5
- Elsewhere: RCSB PDB 6XA6 · PDBe 6XA6 · UniProt Q14160 · UniProt Q9ULK5
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