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Crystal structure of the receptor binding domain of SARS-cov-2 beta variant spike glycoprotein in complex with beta-38

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: 7PS4
Type: protein
Length: 1,266 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike protein S1; Beta-38 Fab heavy chain; Beta-38 Fab light chain
UniProt: P0DTC2
Ligands: NAG, CL
Pockets: 9 · best druggability 0.83

Structure

x-ray diffraction · 6 distinct chains · 10% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Spike protein S1	protein	194	16% helix, 28% strand	P0DTC2
H	Beta-38 Fab heavy chain	protein	223	8% helix, 55% strand	—
L	Beta-38 Fab light chain	protein	213	7% helix, 51% strand	—
A	Spike protein S1	protein	195	13% helix, 31% strand	P0DTC2
B	Beta-38 Fab heavy chain	protein	228	8% helix, 53% strand	—
C	Beta-38 Fab light chain	protein	213	6% helix, 50% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains E, A
CL · Chloride ion · ion · 2 copies · chains H, B, C

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

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1197	0.83	0.84	105	empty
2	956	0.71	0.76	117	empty
3	380	0.60	0.76	47	empty
4	410	0.55	0.73	63	empty
5	227	0.50	0.75	35	empty

Interfaces

11 interfaces between chains.

B–C · 1788 Å² buried · 16 hydrogen bonds · protein-protein
H–L · 1777 Å² buried · 17 hydrogen bonds · protein-protein
E–A · 933 Å² buried · 17 hydrogen bonds · protein-protein
E–H · 596 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 538 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

7PS4 · 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 7PS4 · PDBe 7PS4 · UniProt P0DTC2

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