MolNFT v1 · #101544 · protein

Crystal structure of mouse N-cadherin EC1-2 A78SI92M

4NUM · Cadherin-2: “Crystal structure of mouse N-cadherin EC1-2 A78SI92M”. X-ray diffraction, 1 ligand (CA), 4 pockets (best druggability 0.62). MolNFT v1 #101544 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4NUM
Type: protein
Length: 860 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cadherin-2
UniProt: P15116
Ligands: CA
Pockets: 4 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Cadherin-2	protein	215	3% helix, 45% strand	P15116

Ligands and binding sites

CA · Calcium ion · metal · 12 copies · chains A, B, C, D

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	542	0.62	0.74	57	empty
2	495	0.61	0.75	54	empty
3	165	0.52	0.78	28	empty
4	117	0.42	0.76	17	empty

Interfaces

4 interfaces between chains.

A–B · 874 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 869 Å² buried · 15 hydrogen bonds · protein-protein
B–D · 316 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 299 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4NUM · Crystal structure of mouse N-cadherin EC1-2 A78SI92M · the same entry in another collection · chain D against D, TM-score 1.00
P15116 · AlphaFold monomer V2.0 prediction for cadherin-2 (P15116) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P15116
Elsewhere: RCSB PDB 4NUM · PDBe 4NUM · UniProt P15116

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