MolNFT v1 · #176168 · protein

SARS-COV2 S protein at open state

7DDN · Spike glycoprotein: “SARS-COV2 S protein at open state”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #176168 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7DDN
Type: protein
Length: 3,202 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 · 2 distinct chains · 21% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike glycoprotein	protein	1066	21% helix, 30% strand	P0DTC2
C, B	Spike glycoprotein	protein	1068	21% helix, 31% 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	1002	0.86	0.87	110	empty
2	970	0.85	0.86	97	empty
3	730	0.84	0.87	82	empty
4	372	0.80	0.89	53	empty
5	237	0.79	0.92	34	empty

Interfaces

3 interfaces between chains.

A–B · 5373 Å² buried · 45 hydrogen bonds · protein-protein
C–B · 5313 Å² buried · 50 hydrogen bonds · protein-protein
A–C · 4426 Å² buried · 34 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 39 disulfide (disulfide).

Compared structures

7DDN · SARS-Cov2 S protein at open 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 7DDN · PDBe 7DDN · UniProt P0DTC2

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