Research workbench

SARS-cov-2 spike glycoprotein with 2 rbds erect

Analyse SARS-cov-2 spike glycoprotein with 2 rbds erect in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7A93
Type: protein
Length: 3,221 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike glycoprotein
UniProt: P0DTC2
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 2 distinct chains · 18% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Spike glycoprotein	protein	1074	19% helix, 29% strand	P0DTC2
B	Spike glycoprotein	protein	1073	18% helix, 27% strand	P0DTC2

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	837	0.86	0.88	89	empty
2	850	0.86	0.88	95	empty
3	947	0.81	0.83	99	empty
4	1046	0.79	0.81	90	empty
5	380	0.78	0.87	55	empty

Interfaces

3 interfaces between chains.

A–C · 4567 Å² buried · 30 hydrogen bonds · protein-protein
B–C · 4134 Å² buried · 36 hydrogen bonds · protein-protein
A–B · 4124 Å² buried · 31 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 42 disulfide (disulfide).

Compared structures

7A93 · SARS-CoV-2 Spike Glycoprotein with 2 RBDs Erect · 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 P0DTC2
Elsewhere: RCSB PDB 7A93 · PDBe 7A93 · UniProt P0DTC2

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