MolNFT v1 · #185363 · protein

Crystal structure of the receptor binding domain of SARS-cov-2 beta variant spike glycoprotein in complex with beta-24 fabs

7PS0 · Spike protein S1: “Crystal structure of the receptor binding domain of SARS-cov-2 beta variant spike glycoprotein in complex…”. X-ray diffraction, 2 ligands (NAG, SO4), 18 pockets (best druggability 0.68). MolNFT v1 #185363 on…

PDB: 7PS0
Type: protein
Length: 1,244 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike protein S1; Beta-24 heavy chain; Beta-24 light chain
UniProt: P0DTC2
Ligands: NAG, SO4
Pockets: 18 · best druggability 0.68

Structure

x-ray diffraction · 6 distinct chains · 8% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Spike protein S1	protein	195	12% helix, 29% strand	P0DTC2
H	Beta-24 heavy chain	protein	220	5% helix, 54% strand	—
L	Beta-24 light chain	protein	213	6% helix, 50% strand	—
A	Spike protein S1	protein	183	14% helix, 27% strand	P0DTC2
B	Beta-24 heavy chain	protein	219	5% helix, 55% strand	—
C	Beta-24 light chain	protein	214	6% helix, 50% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E, A
SO4 · Sulfate ion · ion · 6 copies · chains H, L, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	90	0.68	0.93	28	empty
2	466	0.67	0.79	67	SO4
3	83	0.64	0.91	25	empty
4	565	0.60	0.73	54	empty
5	197	0.60	0.81	35	empty

Interfaces

9 interfaces between chains.

H–L · 1862 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 1800 Å² buried · 14 hydrogen bonds · protein-protein
H–A · 565 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 511 Å² buried · 8 hydrogen bonds · protein-protein
E–H · 507 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

7PS0 · Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike… · the same entry in another collection · chain E against E, 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 7PS0 · PDBe 7PS0 · UniProt P0DTC2

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