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Crystal structure of hcgp-39 in complex with chitin tetramer

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

PDB: 1HJV
Type: protein
Length: 1,448 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chitinase-3 like protein 1
UniProt: P36222
Ligands: NAG, SO4
Pockets: 13 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Chitinase-3 like protein 1	protein	362	37% helix, 23% strand	P36222

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 32 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 12 copies · chains A, B, D, C

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

Pockets

13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1183	0.81	0.83	133	SO4
2	52	0.67	0.96	18	empty
3	351	0.67	0.80	47	NAG, SO4
4	272	0.65	0.82	40	NAG
5	227	0.65	0.83	40	empty

Interfaces

6 interfaces between chains.

A–D · 785 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 767 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 302 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 269 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 120 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

1HJV · Crystal structure of hcgp-39 in complex with chitin tetramer · the same entry in another collection · chain D against D, 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 D 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 1HJV · PDBe 1HJV · UniProt P36222

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