MolNFT v1 · #70539 · protein

Crystal structure of E-cadherin EC12 E89A

3LNI · Cadherin-1: “Crystal structure of E-cadherin EC12 E89A”. X-ray diffraction, 1 ligand (CA), 2 pockets (best druggability 0.63). MolNFT v1 #70539 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3LNI
Type: protein
Length: 418 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cadherin-1
UniProt: P09803
Ligands: CA
Pockets: 2 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 0% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cadherin-1	protein	211	0% helix, 44% strand	P09803
B	Cadherin-1	protein	207	0% helix, 45% strand	P09803

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

2 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	366	0.63	0.79	47	empty
2	105	0.40	0.76	18	empty

Interfaces

1 interface between chains.

A–B · 995 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

3LNI · Crystal structure of E-cadherin EC12 E89A · 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 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 P09803
Elsewhere: RCSB PDB 3LNI · PDBe 3LNI · UniProt P09803

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