MolNFT v1 · #53035 · protein

Crystal structure of NCAM2 IG1-3

2WIM · Neural cell adhesion molecule 2: “Crystal structure of NCAM2 IG1-3”. X-ray diffraction, 2 ligands (NAG, CA), 3 pockets (best druggability 0.65). MolNFT v1 #53035 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2WIM
Type: protein
Length: 539 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neural cell adhesion molecule 2
UniProt: O15394
Ligands: NAG, CA
Pockets: 3 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 2% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Neural cell adhesion molecule 2	protein	276	2% helix, 52% strand	O15394
B	Neural cell adhesion molecule 2	protein	263	1% helix, 50% strand	O15394

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
CA · Calcium ion · metal · chains A

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

Pockets

3 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	547	0.65	0.76	34	CA
2	95	0.38	0.75	20	empty
3	55	0.27	0.74	15	empty

Interfaces

1 interface between chains.

A–B · 663 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

2WIM · Crystal structure of NCAM2 IG1-3 · the same entry in another collection · chain A against A, TM-score 1.00
O15394 · AlphaFold monomer V2.0 prediction for neural cell adhesion molecule 2 (O15394) · a predicted model of the same protein · chain B against A, TM-score 0.93

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 O15394
Elsewhere: RCSB PDB 2WIM · PDBe 2WIM · UniProt O15394

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.