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Crystal structure of hcgp-39 in complex with chitin octamer

Analyse Crystal structure of hcgp-39 in complex with chitin octamer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1HJW
Type: protein
Length: 724 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chitinase-3 like protein 1
UniProt: P36222
Ligands: NAG, SO4
Pockets: 6 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Chitinase-3 like protein 1	protein	362	38% helix, 24% strand	P36222

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B
SO4 · Sulfate ion · ion · 4 copies · chains A, B
GOL · Glycerol · additive · 7 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	334	0.67	0.81	42	NAG
2	373	0.65	0.79	50	NAG
3	123	0.55	0.83	29	empty
4	89	0.47	0.81	25	empty
5	58	0.35	0.78	19	empty

Interfaces

1 interface between chains.

A–B · 232 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

1HJW · Crystal structure of hcgp-39 in complex with chitin octamer · the same entry in another collection · chain A against A, TM-score 1.00
P36222 · AlphaFold monomer V2.0 prediction for chitinase-3-like protein 1 (P36222) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P36222
Elsewhere: RCSB PDB 1HJW · PDBe 1HJW · UniProt P36222

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