MolNFT v1 · #152310 · protein

Crystal structure of icchi chitinase from ipomoea carnea

6IDN · Icchi, a glycosylated chitinase: “Crystal structure of icchi chitinase from ipomoea carnea”. X-ray diffraction, 6 ligands (NAG, FUC, BMA), 1 pocket (best druggability 0.36). MolNFT v1 #152310 on GenesisL1: 3D structure, binding…

PDB: 6IDN
Type: protein
Length: 272 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Icchi, a glycosylated chitinase
Ligands: NAG, FUC, BMA, XYP, MAN, CA
Pockets: 1 · best druggability 0.36

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Icchi, a glycosylated chitinase	protein	272	33% helix, 21% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A
BMA · beta-D-mannopyranose · sugar
XYP · beta-D-xylopyranose · sugar
MAN · alpha-D-mannopyranose · sugar
CA · Calcium ion · metal · 2 copies · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	103	0.36	0.74	23	empty

Modifications

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

Compared structures

6IDN · Crystal structure of ICChI chitinase from ipomoea carnea · 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 6IDN · PDBe 6IDN

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