MolNFT v1 · #189821 · protein

SARS-cov-2 kappa variant spike protein in transition state

7VXI · Spike glycoprotein: “SARS-cov-2 kappa variant spike protein in transition state”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #189821 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7VXI
Type: protein
Length: 3,144 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 · 22% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Spike glycoprotein	protein	1062	20% helix, 32% strand	P0DTC2
B	Spike glycoprotein	protein	1020	24% helix, 34% 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	1037	0.86	0.88	132	empty
2	522	0.85	0.91	68	empty
3	1038	0.83	0.84	107	empty
4	878	0.82	0.84	107	empty
5	665	0.82	0.86	89	empty

Interfaces

3 interfaces between chains.

A–B · 5127 Å² buried · 45 hydrogen bonds · protein-protein
A–C · 4708 Å² buried · 37 hydrogen bonds · protein-protein
B–C · 4238 Å² buried · 43 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 37 disulfide (disulfide).

Compared structures

7VXI · SARS-CoV-2 Kappa variant spike protein in transition state · 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 7VXI · PDBe 7VXI · UniProt P0DTC2

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