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Putative receptor-binding domain of bat-derived coronavirus HKU9 spike protein

Analyse Putative receptor-binding domain of bat-derived coronavirus HKU9 spike protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5GYQ
Type: protein
Length: 169 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.1
Source: Bat coronavirus HKU9
Molecule: Spike glycoprotein
UniProt: A3EXG6
Ligands: NAG
Pockets: 1 · best druggability 0.35

Structure

x-ray diffraction · resolution 2.1 · 1 distinct chain · 25% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike glycoprotein	protein	169	25% helix, 32% strand	A3EXG6

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 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	91	0.35	0.74	19	empty

Modifications

Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

5GYQ · Putative receptor-binding domain of bat-derived coronavirus HKU9 spike protein · 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
Every structure of UniProt A3EXG6
Elsewhere: RCSB PDB 5GYQ · PDBe 5GYQ · UniProt A3EXG6

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