Research workbench

X-ray structure of first four repeats of human beta-catenin

Analyse X-ray structure of first four repeats of human beta-catenin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3SLA
Type: protein
Length: 801 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Catenin beta-1
UniProt: P35222
Ligands: NA
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · 5 distinct chains · 78% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Catenin beta-1	protein	166	81% helix, 0% strand	P35222
B	Catenin beta-1	protein	156	79% helix, 0% strand	P35222
C	Catenin beta-1	protein	153	69% helix, 0% strand	P35222
D	Catenin beta-1	protein	164	78% helix, 0% strand	P35222
E	Catenin beta-1	protein	162	80% helix, 0% strand	P35222

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains E
GOL · Glycerol · additive · 8 copies · chains A, D, E

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	183	0.67	0.86	43	empty
2	175	0.41	0.73	24	empty
3	78	0.37	0.77	15	empty
4	53	0.26	0.73	18	empty

Interfaces

7 interfaces between chains.

D–E · 630 Å² buried · 5 hydrogen bonds · protein-protein
B–E · 521 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 517 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 236 Å² buried · 0 hydrogen bonds · protein-protein
C–E · 224 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3SLA · X-ray structure of first four repeats of human beta-catenin · the same entry in another collection · chain E against E, TM-score 1.00
P35222 · AlphaFold monomer V2.0 prediction for catenin beta-1 (P35222) · a predicted model of the same protein · chain D against A, TM-score 0.98

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 P35222
Elsewhere: RCSB PDB 3SLA · PDBe 3SLA · UniProt P35222

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