Research workbench

E-cadherin domains 1 and 2 in complex with calcium

Analyse E-cadherin domains 1 and 2 in complex with calcium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1EDH
Type: protein
Length: 422 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E-cadherin
UniProt: P09803
Ligands: CA, HG
Pockets: 2 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	E-cadherin	protein	211	3% helix, 44% strand	P09803

Ligands and binding sites

CA · Calcium ion · metal · 6 copies · chains A, B
HG · Mercury (II) ion · metal · 2 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	386	0.64	0.78	45	HG
2	215	0.51	0.76	34	empty

Interfaces

1 interface between chains.

A–B · 950 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

1EDH · E-cadherin domains 1 and 2 in complex with calcium · the same entry in another collection · chain A against A, TM-score 1.00
P09803 · AlphaFold monomer V2.0 prediction for cadherin-1 (P09803) · a predicted model of the same protein · chain B 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 P09803
Elsewhere: RCSB PDB 1EDH · PDBe 1EDH · UniProt P09803

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