MolNFT v1 · #12196 · protein

Complex of dc-signr and GLCNAC2MAN3

1K9J · Mdc-SIGN2 type I isoform: “Complex of dc-signr and GLCNAC2MAN3”. X-ray diffraction, 3 ligands (MAN, NAG, CA), 3 pockets (best druggability 0.45). MolNFT v1 #12196 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1K9J
Type: protein
Length: 258 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mdc-SIGN2 type I isoform
Ligands: MAN, NAG, CA
Pockets: 3 · best druggability 0.45

Structure

x-ray diffraction · 2 distinct chains · 23% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mdc-SIGN2 type I isoform	protein	130	23% helix, 30% strand	—
B	Mdc-SIGN2 type I isoform	protein	128	23% helix, 34% strand	—

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
CA · Calcium ion · metal · 3 copies · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	87	0.45	0.80	23	empty
2	53	0.33	0.78	12	empty
3	65	0.29	0.74	14	empty

Interfaces

1 interface between chains.

A–B · 568 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

1K9J · Complex of DC-SIGNR and GlcNAc2Man3 · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 1K9J · PDBe 1K9J

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