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Crystal structure of P120 catenin in complex with E-cadherin

Analyse Crystal structure of P120 catenin in complex with E-cadherin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3L6Y
Type: protein
Length: 1,183 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Catenin delta-1; E-cadherin
UniProt: O60716
Pockets: 13 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 72% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Catenin delta-1	protein	356	73% helix, 0% strand	O60716
B, D, F	E-cadherin	protein	18	17% helix, 0% strand	—
C	Catenin delta-1	protein	376	74% helix, 0% strand	O60716
E	Catenin delta-1	protein	397	73% helix, 0% strand	O60716

Pockets

13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	661	0.69	0.77	57	empty
2	318	0.65	0.81	33	empty
3	439	0.63	0.77	40	empty
4	59	0.60	0.92	25	empty
5	119	0.50	0.80	20	empty

Interfaces

6 interfaces between chains.

C–D · 1294 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 1293 Å² buried · 23 hydrogen bonds · protein-protein
E–F · 1277 Å² buried · 25 hydrogen bonds · protein-protein
C–E · 647 Å² buried · 9 hydrogen bonds · protein-protein
A–E · 466 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

3L6Y · Crystal structure of p120 catenin in complex with E-cadherin · the same entry in another collection · chain F against F, TM-score 1.00
O60716 · AlphaFold monomer V2.0 prediction for catenin delta-1 (O60716) · a predicted model of the same protein · chain A 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 O60716
Elsewhere: RCSB PDB 3L6Y · PDBe 3L6Y · UniProt O60716

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