MolNFT v1 · #122529 · protein

Crystal structure of human desmocollin-1 ectodomain

5IRY: “Crystal structure of human desmocollin-1 ectodomain”. X-ray diffraction, 4 ligands (MAN, NAG, BMA), 2 pockets (best druggability 0.62). MolNFT v1 #122529 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5IRY
Type: protein
Length: 1,078 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Desmocollin-1
UniProt: Q08554
Ligands: MAN, NAG, BMA, CA
Pockets: 2 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain · 1% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Desmocollin-1	protein	539	1% helix, 40% strand	Q08554

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 9 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
BMA · beta-D-mannopyranose · sugar
CA · Calcium ion · metal · 24 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	284	0.62	0.80	21	empty
2	88	0.32	0.73	20	empty

Interfaces

1 interface between chains.

A–B · 760 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 11 glycan, 6 disulfide (O-glycosylation, disulfide, N-glycosylation).

Compared structures

5IRY · Crystal structure of human Desmocollin-1 ectodomain · the same entry in another collection · chain A against A, TM-score 1.00
Q08554 · AlphaFold monomer V2.0 prediction for desmocollin-1 (Q08554) · a predicted model of the same protein · chain A against A, TM-score 0.91

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 Q08554
Elsewhere: RCSB PDB 5IRY · PDBe 5IRY · UniProt Q08554

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