Research workbench

SARS-cov-2 spike D614G variant, minus rbd

Analyse SARS-cov-2 spike D614G variant, minus rbd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6XS6
Type: protein
Length: 2,357 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike glycoprotein
UniProt: P0DTC2
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 2 distinct chains · 24% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Spike glycoprotein	protein	785	24% helix, 28% strand	P0DTC2
C	Spike glycoprotein	protein	787	25% helix, 27% strand	P0DTC2

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1039	0.86	0.87	122	empty
2	857	0.82	0.84	63	empty
3	573	0.75	0.82	43	empty
4	574	0.75	0.82	43	empty
5	619	0.75	0.81	45	empty

Interfaces

3 interfaces between chains.

A–C · 3894 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 3854 Å² buried · 30 hydrogen bonds · protein-protein
B–C · 3814 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 27 disulfide (disulfide).

Compared structures

6XS6 · SARS-CoV-2 Spike D614G variant, minus RBD · 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 6XS6 · PDBe 6XS6 · UniProt P0DTC2

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.