MolNFT v1 · #157220 · protein

Crystal structure of the human scribble PDZ1 domain bound to the PDZ- binding motif of apc

6MS1 · Protein scribble homolog: “Crystal structure of the human scribble PDZ1 domain bound to the PDZ- binding motif of apc”. X-ray diffraction, 2 pockets (best druggability 0.42). MolNFT v1 #157220 on GenesisL1: 3D structure, binding…

PDB: 6MS1
Type: protein
Length: 204 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein scribble homolog; Apc C-terminus peptide
UniProt: Q14160
Pockets: 2 · best druggability 0.42

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protein scribble homolog	protein	94	14% helix, 43% strand	Q14160
C, D	Apc C-terminus peptide	protein	8	0% helix, 50% strand	—

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 5 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	100	0.42	0.78	28	empty
2	59	0.31	0.76	18	empty

Interfaces

4 interfaces between chains.

A–D · 524 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 491 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 281 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 177 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6MS1 · Crystal structure of the human Scribble PDZ1 domain bound to the PDZ-binding motif of APC · the same entry in another collection · chain A against A, 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 0.95

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 6MS1 · PDBe 6MS1 · UniProt Q14160

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