MolNFT v1 · #139114 · protein

Prefusion structure of SARS-cov spike glycoprotein, conformation 2

5X5B: “Prefusion structure of SARS-cov spike glycoprotein, conformation 2”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #139114 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5X5B
Type: protein
Length: 3,139 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike glycoprotein
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 2 distinct chains · 19% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike glycoprotein	protein	1033	19% helix, 25% strand	—
B, C	Spike glycoprotein	protein	1053	19% helix, 23% strand	—

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	1072	0.86	0.87	134	empty
2	1010	0.84	0.85	113	empty
3	946	0.83	0.84	93	empty
4	524	0.78	0.85	49	empty
5	121	0.77	0.96	25	empty

Interfaces

3 interfaces between chains.

A–C · 5775 Å² buried · 52 hydrogen bonds · protein-protein
B–C · 5558 Å² buried · 37 hydrogen bonds · protein-protein
A–B · 4505 Å² buried · 47 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide (disulfide).

Compared structures

5X5B · Prefusion structure of SARS-CoV spike glycoprotein, conformation 2 · 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
Elsewhere: RCSB PDB 5X5B · PDBe 5X5B

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