Research workbench

SARS-COV2 S protein at close state

Analyse SARS-COV2 S protein at close state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7DDD
Type: protein
Length: 3,264 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike glycoprotein
UniProt: P0DTC2
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 1 distinct chain · 20% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Spike glycoprotein	protein	1088	20% 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	1014	0.88	0.90	139	empty
2	1021	0.88	0.90	133	empty
3	1017	0.88	0.89	134	empty
4	572	0.84	0.89	85	empty
5	338	0.83	0.92	55	empty

Interfaces

3 interfaces between chains.

A–B · 7664 Å² buried · 82 hydrogen bonds · protein-protein
A–C · 7661 Å² buried · 81 hydrogen bonds · protein-protein
B–C · 7661 Å² buried · 83 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 42 disulfide (disulfide).

Compared structures

7DDD · SARS-Cov2 S protein at close state · 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 7DDD · PDBe 7DDD · UniProt P0DTC2

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