Research workbench

S protein of SARS-cov-2 in complex bound with P5A-2G9

Analyse S protein of SARS-cov-2 in complex bound with P5A-2G9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7CZT
Type: protein
Length: 3,872 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike glycoprotein; Immunoglobulin heavy variable 3-33,CHAINH of P5A-2G9, immunoglobulin…
UniProt: P0DTC2, P01772, P0DOX5, A0A5C2GMM2, Q8N5F4
Ligands: NAG
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 5 distinct chains · 18% helix, 34% 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, I	Immunoglobulin heavy variable 3-33,CHAINH of P5A-2G9, immunoglobulin gamma-1 heavy chain	protein	221	4% helix, 48% strand	P01772, P0DOX5
L, M	Ig C689_LIGHT_IGLV5-37_IGLJ3,IGL@ protein	protein	219	6% helix, 44% strand	A0A5C2GMM2, Q8N5F4

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	792	0.81	0.84	84	empty
2	858	0.81	0.83	69	empty
3	352	0.78	0.88	57	empty
4	256	0.75	0.88	43	empty
5	300	0.74	0.87	46	empty

Interfaces

11 interfaces between chains.

B–C · 4530 Å² buried · 33 hydrogen bonds · protein-protein
A–B · 4234 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 4100 Å² buried · 38 hydrogen bonds · protein-protein
H–L · 1784 Å² buried · 4 hydrogen bonds · protein-protein
I–M · 1770 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

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

Compared structures

7CZT · S protein of SARS-CoV-2 in complex bound with P5A-2G9 · the same entry in another collection · chain M against M, TM-score 1.00
P01772 · AlphaFold monomer V2.0 prediction for immunoglobulin heavy variable 3-33 (P01772) · a predicted model of the same protein · chain H against A, TM-score 0.43

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 P01772
Every structure of UniProt P0DOX5
Every structure of UniProt A0A5C2GMM2
Every structure of UniProt Q8N5F4
Elsewhere: RCSB PDB 7CZT · PDBe 7CZT · UniProt P0DTC2 · UniProt P01772 · UniProt P0DOX5 · UniProt A0A5C2GMM2 · UniProt Q8N5F4

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