Research workbench

SARS-cov-2 omicron S-open

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

PDB: 7WK3
Type: protein
Length: 3,162 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike glycoprotein
UniProt: P0DTC2
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 2 distinct chains · 20% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike glycoprotein	protein	1048	20% helix, 32% strand	P0DTC2
B, C	Spike glycoprotein	protein	1057	21% helix, 32% 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	1022	0.89	0.90	104	empty
2	909	0.85	0.87	100	empty
3	1051	0.82	0.83	97	empty
4	1154	0.78	0.80	114	empty
5	380	0.77	0.87	50	empty

Interfaces

3 interfaces between chains.

A–B · 4761 Å² buried · 42 hydrogen bonds · protein-protein
B–C · 4749 Å² buried · 50 hydrogen bonds · protein-protein
A–C · 4101 Å² buried · 41 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 39 disulfide (disulfide).

Compared structures

7WK3 · SARS-CoV-2 Omicron S-open · 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 7WK3 · PDBe 7WK3 · UniProt P0DTC2

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