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Crystal structure of human E-cadherin (residues 3-213) in X-dimer conformation

Analyse Crystal structure of human E-cadherin (residues 3-213) in X-dimer conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ZT1
Type: protein
Length: 418 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cadherin-1
UniProt: P12830
Ligands: CA
Pockets: 1 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cadherin-1	protein	209	4% helix, 45% strand	P12830

Ligands and binding sites

CA · Calcium ion · metal · 6 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	552	0.66	0.76	66	empty

Interfaces

1 interface between chains.

A–B · 874 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

4ZT1 · Crystal structure of human E-Cadherin (residues 3-213) in x-dimer conformation · the same entry in another collection · chain A against A, TM-score 1.00
P12830 · AlphaFold monomer V2.0 prediction for cadherin-1 (P12830) · 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 P12830
Elsewhere: RCSB PDB 4ZT1 · PDBe 4ZT1 · UniProt P12830

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