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Mapping neutralizing and immunodominant sites on the SARS-cov-2 spike receptor-binding domain by structure-guided high-resolution serology

Analyse Mapping neutralizing and immunodominant sites on the SARS-cov-2 spike… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7JXE
Type: protein
Length: 447 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: S2X35 antigen-binding (Fab) fragment
Pockets: 4 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	S2X35 antigen-binding (Fab) fragment	protein	231	10% helix, 48% strand	—
L	S2X35 antigen-binding (Fab) fragment	protein	216	8% helix, 50% strand	—

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	528	0.60	0.74	56	empty
2	171	0.51	0.78	32	empty
3	112	0.42	0.77	24	empty
4	78	0.33	0.75	19	empty

Interfaces

1 interface between chains.

H–L · 1845 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

7JXE · Mapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding… · 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 7JXE · PDBe 7JXE

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