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Cryoem structure of SARS-cov-2 spike protein (S-6P, 1-up) in complex with sybodies (SB45)

Analyse Cryoem structure of SARS-cov-2 spike protein (S-6P, 1-up) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7N0G
Type: protein
Length: 3,592 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike glycoprotein; Synthetic nanobody (sybody), SB45
UniProt: P0DTC2
Ligands: NAG
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 4 distinct chains · 20% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike glycoprotein	protein	1076	20% helix, 32% strand	P0DTC2
B	Spike glycoprotein	protein	1078	20% helix, 34% strand	P0DTC2
C	Spike glycoprotein	protein	1075	21% helix, 34% strand	P0DTC2
X, Y, Z	Synthetic nanobody (sybody), SB45	protein	121	2% helix, 57% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 73 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

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	891	0.85	0.87	124	empty
2	559	0.83	0.89	59	empty
3	1090	0.83	0.84	112	empty
4	651	0.83	0.87	62	empty
5	1083	0.82	0.83	88	empty

Interfaces

9 interfaces between chains.

B–C · 4979 Å² buried · 43 hydrogen bonds · protein-protein
A–C · 4762 Å² buried · 43 hydrogen bonds · protein-protein
A–B · 4627 Å² buried · 43 hydrogen bonds · protein-protein
B–Y · 1145 Å² buried · 19 hydrogen bonds · protein-protein
A–X · 1134 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 56 glycan, 42 disulfide (N-glycosylation, disulfide, glycation).

Compared structures

7N0G · CryoEm structure of SARS-CoV-2 spike protein (S-6P, 1-up) in complex with sybodies (Sb45) · 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 7N0G · PDBe 7N0G · UniProt P0DTC2

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