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Crystal structure of a SARS-cov-2 cross-neutralizing antibody COVA1-16 Fab

Analyse Crystal structure of a SARS-cov-2 cross-neutralizing antibody COVA1-16 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7JMX
Type: protein
Length: 430 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: COVA1-16 heavy chain; COVA1-16 light chain
Ligands: SO4
Pockets: 3 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	COVA1-16 heavy chain	protein	222	9% helix, 50% strand	—
L	COVA1-16 light chain	protein	208	7% helix, 51% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains H
ACT · Acetate ion · additive · chains H

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	602	0.62	0.74	59	empty
2	92	0.36	0.75	23	empty
3	59	0.29	0.75	17	empty

Interfaces

1 interface between chains.

H–L · 1767 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7JMX · Crystal structure of a SARS-CoV-2 cross-neutralizing antibody COVA1-16 Fab · the same entry in another collection · chain H against H, 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
Elsewhere: RCSB PDB 7JMX · PDBe 7JMX

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