MolNFT v1 · #120041 · protein

Crystal structure of the receptor binding domain of the spike glycoprotein of human betacoronavirus HKU1 (HKU1 1A-ctd, 2.3 ångström, native-sad phasing)

5GNB: “Crystal structure of the receptor binding domain of the spike glycoprotein of human betacoronavirus HKU1…”. X-ray diffraction, 1 ligand (NAG), 1 pocket (best druggability 0.48). MolNFT v1 #120041 on GenesisL1: 3D structure, binding…

PDB: 5GNB
Type: protein
Length: 364 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike glycoprotein
UniProt: Q5MQD0
Ligands: NAG
Pockets: 1 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 15% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike glycoprotein	protein	364	15% helix, 35% strand	Q5MQD0

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 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	168	0.48	0.77	30	empty

Modifications

Observed in the structure: 11 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

5GNB · Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human… · 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 Q5MQD0
Elsewhere: RCSB PDB 5GNB · PDBe 5GNB · UniProt Q5MQD0

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