Research workbench

S protein of SARS-cov-2 in complex bound with P2B-1A10

Analyse S protein of SARS-cov-2 in complex bound with P2B-1A10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7CZQ
Type: protein
Length: 3,868 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike glycoprotein; Ig C642_HEAVY_IGHV3-53_IGHD1-26_IGHJ6,CHAIN H of P2B-1A10…
UniProt: P0DTC2, A0A5C2GF00, P0DOX5, P01594, Q8TCD0
Ligands: NAG
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 5 distinct chains · 18% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike glycoprotein	protein	1006	21% helix, 34% strand	P0DTC2
B	Spike glycoprotein	protein	982	19% helix, 31% strand	P0DTC2
C	Spike glycoprotein	protein	1004	21% helix, 31% strand	P0DTC2
H, J	Ig C642_HEAVY_IGHV3-53_IGHD1-26_IGHJ6,CHAIN H of P2B-1A10, immunoglobulin gamma-1 heavy chain	protein	223	3% helix, 47% strand	A0A5C2GF00, P0DOX5
K, N	Immunoglobulin kappa variable 1-33,UNCHARACTERIZED protein	protein	215	5% helix, 37% strand	P01594, Q8TCD0

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 70 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	1033	0.85	0.86	127	empty
2	630	0.81	0.86	73	empty
3	815	0.81	0.84	87	empty
4	1189	0.78	0.80	94	empty
5	76	0.74	0.97	22	empty

Interfaces

11 interfaces between chains.

B–C · 4501 Å² buried · 33 hydrogen bonds · protein-protein
A–B · 4271 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 4134 Å² buried · 39 hydrogen bonds · protein-protein
J–N · 1927 Å² buried · 13 hydrogen bonds · protein-protein
H–K · 1919 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 48 glycan, 44 disulfide (N-glycosylation, disulfide).

Compared structures

7CZQ · S protein of SARS-CoV-2 in complex bound with P2B-1A10 · the same entry in another collection · chain N against N, TM-score 1.00
P01594 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa variable 1-33 (P01594) · a predicted model of the same protein · chain K against A, TM-score 0.42

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
Every structure of UniProt A0A5C2GF00
Every structure of UniProt P0DOX5
Every structure of UniProt P01594
Every structure of UniProt Q8TCD0
Elsewhere: RCSB PDB 7CZQ · PDBe 7CZQ · UniProt P0DTC2 · UniProt A0A5C2GF00 · UniProt P0DOX5 · UniProt P01594 · UniProt Q8TCD0

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