MolNFT v1 · #178866 · protein

Crystal structure of human scribble PDZ2

7JO7 · Protein scribble homolog: “Crystal structure of human scribble PDZ2”. X-ray diffraction, 4 pockets (best druggability 0.77). MolNFT v1 #178866 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7JO7
Type: protein
Length: 367 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein scribble homolog
UniProt: Q14160
Pockets: 4 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 12% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein scribble homolog	protein	91	15% helix, 33% strand	Q14160
B	Protein scribble homolog	protein	90	10% helix, 40% strand	Q14160
C	Protein scribble homolog	protein	93	9% helix, 44% strand	Q14160
D	Protein scribble homolog	protein	93	15% helix, 37% strand	Q14160

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 2 copies · chains A, C

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	993	0.77	0.79	124	empty
2	144	0.44	0.76	36	empty
3	114	0.44	0.77	27	empty
4	101	0.39	0.76	25	empty

Interfaces

6 interfaces between chains.

A–D · 426 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 360 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 346 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 336 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 204 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

7JO7 · Crystal Structure of Human Scribble PDZ2 · 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 A against A, TM-score 0.96

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 7JO7 · PDBe 7JO7 · UniProt Q14160

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