MolNFT v1 · #118084 · protein

Crystal structure of human desmoglein-2 ectodomain

5ERD: “Crystal structure of human desmoglein-2 ectodomain”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 2 pockets (best druggability 0.65). MolNFT v1 #118084 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ERD
Type: protein
Length: 1,113 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Desmoglein-2
UniProt: Q14126
Ligands: NAG, MAN, BMA, FUC, CA
Pockets: 2 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 2% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Desmoglein-2	protein	554	1% helix, 41% strand	Q14126
B	Desmoglein-2	protein	559	3% helix, 41% strand	Q14126

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, B
MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 4 copies
FUC · alpha-L-fucopyranose · sugar · chains A
CA · Calcium ion · metal · 22 copies · chains A, B
EDO · 1,2-ethanediol · additive · chains A

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	481	0.65	0.77	42	empty
2	52	0.46	0.85	16	empty

Interfaces

1 interface between chains.

A–B · 649 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 17 glycan, 6 disulfide, 1 covalent (N-glycosylation, disulfide, O-glycosylation, additive adduct, glycosylation).

Compared structures

5ERD · Crystal structure of human Desmoglein-2 ectodomain · the same entry in another collection · chain A against A, TM-score 1.00
Q14126 · AlphaFold monomer V2.0 prediction for desmoglein-2 (Q14126) · a predicted model of the same protein · chain A against A, TM-score 0.86

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 Q14126
Elsewhere: RCSB PDB 5ERD · PDBe 5ERD · UniProt Q14126

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