Research workbench

SARS-cov-2 U1S2Q 1-rbd up spike protein trimer

Analyse SARS-cov-2 U1S2Q 1-rbd up spike protein trimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6X2A
Type: protein
Length: 2,875 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike glycoprotein
UniProt: P0DTC2
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 3 distinct chains · 24% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike glycoprotein	protein	966	24% helix, 30% strand	P0DTC2
B	Spike glycoprotein	protein	948	24% helix, 31% strand	P0DTC2
C	Spike glycoprotein	protein	961	23% helix, 32% strand	P0DTC2

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	732	0.83	0.87	68	empty
2	1108	0.83	0.84	103	empty
3	696	0.81	0.85	76	empty
4	569	0.80	0.86	51	empty
5	773	0.80	0.83	73	empty

Interfaces

3 interfaces between chains.

A–C · 4978 Å² buried · 47 hydrogen bonds · protein-protein
A–B · 4667 Å² buried · 54 hydrogen bonds · protein-protein
B–C · 4515 Å² buried · 37 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 34 disulfide (disulfide).

Compared structures

6X2A · SARS-CoV-2 u1S2q 1-RBD Up Spike Protein Trimer · 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 6X2A · PDBe 6X2A · UniProt P0DTC2

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