Research workbench

Crystal structure of the receptor binding domain of SARS-cov-2 spike glycoprotein in complex with covox-158 Fab (crystal form 1)

Analyse Crystal structure of the receptor binding domain of SARS-cov-2 spike… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7BEJ
Type: protein
Length: 623 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Covox-158 heavy chain; Covox-158 light chain; Spike glycoprotein
UniProt: P0DTC2
Ligands: NAG, FUC
Pockets: 7 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Covox-158 heavy chain	protein	215	9% helix, 53% strand	—
L	Covox-158 light chain	protein	213	6% helix, 51% strand	—
E	Spike glycoprotein	protein	195	14% helix, 31% strand	P0DTC2

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E
FUC · alpha-L-fucopyranose · sugar
FMT · Formic acid · additive · 6 copies · chains L, E
GOL · Glycerol · additive · 2 copies · chains H, L, E

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

Pockets

7 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	650	0.63	0.74	66	empty
2	167	0.59	0.83	27	empty
3	61	0.54	0.88	22	GOL
4	212	0.49	0.76	31	empty
5	136	0.42	0.75	25	empty

Interfaces

3 interfaces between chains.

H–L · 1717 Å² buried · 18 hydrogen bonds · protein-protein
H–E · 697 Å² buried · 14 hydrogen bonds · protein-protein
L–E · 509 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

7BEJ · Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in… · the same entry in another collection · chain H against H, 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 P0DTC2
Elsewhere: RCSB PDB 7BEJ · PDBe 7BEJ · UniProt P0DTC2

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.