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Minor cryo-EM structure of S protein trimer of SARS-COV2 with K-874A vhh, composite MAP

Analyse Minor cryo-EM structure of S protein trimer of SARS-COV2 with K-874A vhh… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7FG2
Type: protein
Length: 1,202 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike glycoprotein; K-874A vhh
UniProt: P0DTC2
Pockets: 12 · best druggability 0.72

Structure

electron microscopy · 2 distinct chains · 18% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike glycoprotein	protein	1086	20% helix, 21% strand	P0DTC2
D	K-874A vhh	protein	116	3% helix, 34% strand	—

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	279	0.72	0.86	36	empty
2	327	0.64	0.80	41	empty
3	143	0.64	0.86	20	empty
4	180	0.57	0.81	39	empty
5	83	0.57	0.86	20	empty

Interfaces

1 interface between chains.

A–D · 675 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

7FG2 · Minor cryo-EM structure of S protein trimer of SARS-CoV2 with K-874A VHH, composite map · 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 7FG2 · PDBe 7FG2 · UniProt P0DTC2

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