MolNFT v1 · #189817 · protein

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

7VXE · Spike glycoprotein: “SARS-cov-2 kappa variant spike protein in open state”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #189817 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7VXE
Type: protein
Length: 3,186 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 · 1 distinct chain · 20% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Spike glycoprotein	protein	1062	20% helix, 31% 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	885	0.86	0.88	116	empty
2	756	0.85	0.88	99	empty
3	540	0.85	0.91	75	empty
4	1096	0.82	0.83	112	empty
5	1119	0.80	0.82	97	empty

Interfaces

3 interfaces between chains.

B–C · 4848 Å² buried · 44 hydrogen bonds · protein-protein
A–B · 4825 Å² buried · 37 hydrogen bonds · protein-protein
A–C · 4423 Å² buried · 38 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 39 disulfide (disulfide).

Compared structures

7VXE · SARS-CoV-2 Kappa variant spike protein in open 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 7VXE · PDBe 7VXE · UniProt P0DTC2

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