Research workbench

SARS-cov-2 omicron S-open-2

Analyse SARS-cov-2 omicron S-open-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7WVO
Type: protein
Length: 2,961 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 · 3 distinct chains · 19% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike glycoprotein	protein	1048	18% helix, 30% strand	P0DTC2
B	Spike glycoprotein	protein	1057	19% helix, 30% strand	P0DTC2
C	Spike glycoprotein	protein	856	21% helix, 30% 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	1191	0.86	0.87	139	empty
2	382	0.84	0.93	58	empty
3	396	0.84	0.92	40	empty
4	621	0.79	0.85	67	empty
5	804	0.79	0.82	78	empty

Interfaces

3 interfaces between chains.

A–B · 5258 Å² buried · 36 hydrogen bonds · protein-protein
A–C · 4527 Å² buried · 41 hydrogen bonds · protein-protein
B–C · 4304 Å² buried · 30 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 35 disulfide (disulfide).

Compared structures

7WVO · SARS-CoV-2 Omicron S-open-2 · 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 7WVO · PDBe 7WVO · UniProt P0DTC2

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