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Crystal structure of human nectin-3 full ectodomain (D1-D3)

Analyse Crystal structure of human nectin-3 full ectodomain (D1-D3) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4FOM
Type: protein
Length: 302 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Poliovirus receptor-related protein 3
UniProt: Q9NQS3
Ligands: NAG, MAN, BMA, FUC

Structure

x-ray diffraction · 1 distinct chain · 2% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Poliovirus receptor-related protein 3	protein	302	2% helix, 49% strand	Q9NQS3

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A
MAN · alpha-D-mannopyranose · sugar · 6 copies
BMA · beta-D-mannopyranose · sugar · 4 copies
FUC · alpha-L-fucopyranose · sugar · chains A

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

Modifications

Observed in the structure: 5 glycan, 2 disulfide (N-glycosylation, disulfide).

Compared structures

4FOM · Crystal structure of human nectin-3 full ectodomain (D1-D3) · the same entry in another collection · chain A against A, TM-score 1.00
Q9NQS3 · AlphaFold monomer V2.0 prediction for nectin-3 (Q9NQS3) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q9NQS3
Elsewhere: RCSB PDB 4FOM · PDBe 4FOM · UniProt Q9NQS3

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