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Crystal structure of the receptor binding domain of SARS-cov-2 beta variant spike glycoprotein in complex with beta-22 fabs

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

PDB: 7PRZ
Type: protein
Length: 640 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-22 Fab heavy chain; Spike protein S1; Beta-22 Fab light chain
UniProt: P0DTC2
Ligands: NAG, FUC, SO4
Pockets: 6 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Beta-22 Fab heavy chain	protein	225	7% helix, 50% strand	—
E	Spike protein S1	protein	198	15% helix, 27% strand	P0DTC2
L	Beta-22 Fab light chain	protein	217	6% helix, 52% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains E, L
FUC · alpha-L-fucopyranose · sugar · 2 copies · chains L
SO4 · Sulfate ion · ion · 15 copies · chains H, E, L

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	369	0.68	0.82	49	FUC, SO4
2	441	0.58	0.74	54	SO4
3	84	0.44	0.79	19	empty
4	103	0.38	0.75	23	empty
5	75	0.32	0.74	17	empty

Interfaces

3 interfaces between chains.

H–L · 1981 Å² buried · 12 hydrogen bonds · protein-protein
H–E · 826 Å² buried · 13 hydrogen bonds · protein-protein
E–L · 163 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

7PRZ · Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike… · 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 7PRZ · PDBe 7PRZ · UniProt P0DTC2

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