MolNFT v1 · #190334 · protein

SARS-cov-2 omicron S-open

7WVN · Spike glycoprotein: “SARS-cov-2 omicron S-open”. Electron microscopy, 20 pockets (best druggability 0.89). MolNFT v1 #190334 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7WVN
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 · 19% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike glycoprotein	protein	1048	18% helix, 30% strand	P0DTC2
B, C	Spike glycoprotein	protein	1057	19% helix, 29% 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	805	0.89	0.92	91	empty
2	985	0.86	0.87	122	empty
3	830	0.83	0.85	87	empty
4	510	0.78	0.85	75	empty
5	540	0.77	0.84	74	empty

Interfaces

3 interfaces between chains.

B–C · 5329 Å² buried · 44 hydrogen bonds · protein-protein
A–B · 5261 Å² buried · 36 hydrogen bonds · protein-protein
A–C · 4565 Å² buried · 39 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 39 disulfide (disulfide).

Compared structures

7WVN · 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 7WVN · PDBe 7WVN · UniProt P0DTC2

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