Research workbench

SARS-cov-2 S trimer, S-open

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

PDB: 7DK3
Type: protein
Length: 3,172 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike glycoprotein
UniProt: P0DTC2
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 2 distinct chains · 21% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Spike glycoprotein	protein	1062	21% helix, 32% strand	P0DTC2
C	Spike glycoprotein	protein	1048	22% 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	811	0.84	0.87	93	empty
2	668	0.81	0.85	70	empty
3	559	0.81	0.87	78	empty
4	678	0.80	0.85	68	empty
5	207	0.78	0.92	43	empty

Interfaces

3 interfaces between chains.

B–C · 5543 Å² buried · 61 hydrogen bonds · protein-protein
A–B · 5535 Å² buried · 44 hydrogen bonds · protein-protein
A–C · 4938 Å² buried · 46 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 38 disulfide (disulfide).

Compared structures

7DK3 · SARS-CoV-2 S trimer, 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 7DK3 · PDBe 7DK3 · UniProt P0DTC2

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