MolNFT v1 · #137698 · protein

Crystal structure of human scribble PDZ1:BETA-pix complex

5VWK · Protein scribble homolog: “Crystal structure of human scribble PDZ1:BETA-pix complex”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.84). MolNFT v1 #137698 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5VWK
Type: protein
Length: 438 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein scribble homolog; Beta-pix
UniProt: Q14160
Ligands: SO4
Pockets: 6 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 12% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protein scribble homolog	protein	102	13% helix, 41% strand	Q14160
C, D	Protein scribble homolog	protein	101	13% helix, 41% strand	Q14160
E, F, G, H	Beta-pix	protein	8	0% helix, 38% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 12 copies · chains A, C, G, B, D, H, F, E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1007	0.84	0.86	106	SO4
2	207	0.65	0.84	22	empty
3	97	0.56	0.85	24	SO4
4	94	0.53	0.84	22	SO4
5	79	0.48	0.82	20	empty

Interfaces

22 interfaces between chains.

D–E · 576 Å² buried · 15 hydrogen bonds · protein-protein
C–F · 574 Å² buried · 18 hydrogen bonds · protein-protein
A–H · 545 Å² buried · 11 hydrogen bonds · protein-protein
B–G · 541 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 260 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5VWK · Crystal structure of human Scribble PDZ1:Beta-PIX 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 0.91

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 5VWK · PDBe 5VWK · UniProt Q14160

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