MolNFT v1 · #68215 · protein

Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer

3JCL: “Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #68215 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3JCL
Type: protein
Length: 3,201 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike glycoprotein
UniProt: P11224
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 1 distinct chain · 28% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Spike glycoprotein	protein	1067	28% helix, 29% strand	P11224

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	533	0.84	0.90	84	empty
2	697	0.84	0.88	87	empty
3	506	0.83	0.89	71	empty
4	411	0.83	0.91	60	empty
5	455	0.82	0.90	68	empty

Interfaces

3 interfaces between chains.

B–C · 4152 Å² buried · 31 hydrogen bonds · protein-protein
A–B · 4144 Å² buried · 31 hydrogen bonds · protein-protein
A–C · 4142 Å² buried · 31 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 54 disulfide (disulfide).

Compared structures

3JCL · Cryo-electron microscopy structure of a coronavirus spike glycoprotein 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 P11224
Elsewhere: RCSB PDB 3JCL · PDBe 3JCL · UniProt P11224

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