Research workbench

Cryo-EM structure of SARS-CoV-2 ORF3a

Analyse Cryo-EM structure of SARS-CoV-2 ORF3a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7KJR
Type: protein
Length: 448 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.08
Source: Homo sapiens; Severe acute respiratory syndrome coronavirus 2
Molecule: ORF3a protein; Apolipoprotein A-I
UniProt: P0DTC3, P02647
Ligands: PEE
Pockets: 3 · best druggability 0.85

Structure

electron microscopy · resolution 2.08 · 2 distinct chains · 52% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	ORF3a protein	protein	193	46% helix, 26% strand	P0DTC3
C, D	Apolipoprotein A-I	protein	31	94% helix, 0% strand	P02647

Ligands and binding sites

PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 2 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1111	0.85	0.86	103	PEE
2	173	0.43	0.74	33	empty
3	54	0.30	0.76	17	empty

Interfaces

5 interfaces between chains.

A–B · 2608 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 300 Å² buried · 1 hydrogen bond · protein-protein
B–D · 288 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 285 Å² buried · 1 hydrogen bond · protein-protein
A–C · 277 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

7KJR · Cryo-EM structure of SARS-cov-2 ORF3A · the same entry in another collection · chain A against A, TM-score 1.00
P02647 · AlphaFold monomer V2.0 prediction for apolipoprotein a-I (P02647) · a predicted model of the same protein · chain C against A, TM-score 0.75

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 P0DTC3
Every structure of UniProt P02647
Elsewhere: RCSB PDB 7KJR · PDBe 7KJR · UniProt P0DTC3 · UniProt P02647

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