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Structural basis for a germline-biased antibody response to SARS-cov-2 (RBD:C1A-C2 Fab)

Analyse Structural basis for a germline-biased antibody response to SARS-cov-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7KFX
Type: protein
Length: 634 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike glycoprotein; Heavy chain of human antibody C1A-C2 Fab; Light chain of human…
UniProt: P0DTC2
Ligands: NAG
Pockets: 5 · best druggability 0.59

Structure

x-ray diffraction · 3 distinct chains · 10% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike glycoprotein	protein	195	18% helix, 29% strand	P0DTC2
H	Heavy chain of human antibody C1A-C2 Fab	protein	225	7% helix, 48% strand	—
L	Light chain of human antibody C1A-C2 Fab	protein	214	6% helix, 50% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A

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

Pockets

5 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	266	0.59	0.79	38	empty
2	141	0.53	0.81	26	empty
3	271	0.49	0.74	33	empty
4	80	0.39	0.78	19	empty
5	66	0.28	0.73	17	empty

Interfaces

3 interfaces between chains.

H–L · 1924 Å² buried · 18 hydrogen bonds · protein-protein
A–H · 916 Å² buried · 23 hydrogen bonds · protein-protein
A–L · 419 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

7KFX · Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-C2 Fab) · 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 7KFX · PDBe 7KFX · UniProt P0DTC2

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