MolNFT v1 · #169382 · protein

Crystal structure of human scribble PDZ2:VANGL2 complex

6XA7 · Protein scribble homolog: “Crystal structure of human scribble PDZ2:VANGL2 complex”. X-ray diffraction, 4 pockets (best druggability 0.72). MolNFT v1 #169382 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6XA7
Type: protein
Length: 393 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein scribble homolog; Vang-like protein 2
UniProt: Q14160, Q9ULK5
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 7 distinct chains · 15% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein scribble homolog	protein	93	15% helix, 40% strand	Q14160
B	Protein scribble homolog	protein	96	17% helix, 41% strand	Q14160
C	Protein scribble homolog	protein	92	15% helix, 37% strand	Q14160
D	Protein scribble homolog	protein	91	15% helix, 33% strand	Q14160
E, H	Vang-like protein 2	protein	6	0% helix, 50% strand	Q9ULK5
F	Vang-like protein 2	protein	4	0% helix, 50% strand	Q9ULK5
G	Vang-like protein 2	protein	5	0% helix, 60% strand	Q9ULK5

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 7 copies · chains B, C, A, D, G

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	575	0.72	0.80	54	EDO
2	112	0.41	0.76	24	empty
3	78	0.35	0.76	22	empty
4	59	0.29	0.75	17	empty

Interfaces

11 interfaces between chains.

C–G · 401 Å² buried · 8 hydrogen bonds · protein-protein
D–H · 394 Å² buried · 13 hydrogen bonds · protein-protein
A–E · 394 Å² buried · 11 hydrogen bonds · protein-protein
B–F · 355 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 340 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6XA7 · Crystal Structure of Human Scribble PDZ2:Vangl2 complex · the same entry in another collection · chain H against H, TM-score 1.00
Q14160 · AlphaFold monomer V2.0 prediction for protein scribble homolog (Q14160) · a predicted model of the same protein · chain C against A, TM-score 0.98
Q9ULK5 · AlphaFold monomer V2.0 prediction for vang-like protein 2 (Q9ULK5) · a predicted model of the same protein · chain F against A, TM-score 0.97

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 6XA7 · PDBe 6XA7 · UniProt Q14160 · UniProt Q9ULK5

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