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Potent SARS-cov-2 binding and neutralization through maturation of iconic SARS-cov-1ANTIBODIES

Analyse Potent SARS-cov-2 binding and neutralization through maturation of iconic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7KZB
Type: protein
Length: 992 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab heavy chain of CR3014-C8 antibody; Fab light chain of CR3014-C8 antibody; Spike…
UniProt: P0DTC2
Ligands: NAG, FUC, CL
Pockets: 11 · best druggability 0.64

Structure

x-ray diffraction · 5 distinct chains · 7% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab heavy chain of CR3014-C8 antibody	protein	214	8% helix, 50% strand	—
L	Fab light chain of CR3014-C8 antibody	protein	214	5% helix, 51% strand	—
C	Spike glycoprotein	protein	192	19% helix, 28% strand	P0DTC2
A	Fab heavy chain of CR3022-B6 antibody	protein	170	0% helix, 38% strand	—
B	Fab light chain of CR3022-B6 antibody	protein	202	3% helix, 42% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains C
FUC · alpha-L-fucopyranose · sugar
CL · Chloride ion · ion · chains L

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

Pockets

11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	332	0.64	0.80	69	empty
2	394	0.63	0.78	44	empty
3	321	0.59	0.77	43	empty
4	144	0.55	0.81	26	empty
5	63	0.51	0.86	19	empty

Interfaces

6 interfaces between chains.

H–L · 1682 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1169 Å² buried · 3 hydrogen bonds · protein-protein
C–B · 538 Å² buried · 9 hydrogen bonds · protein-protein
L–C · 499 Å² buried · 8 hydrogen bonds · protein-protein
H–C · 268 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

7KZB · Potent SARS-CoV-2 binding and neutralization through maturation of iconic… · 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
Every structure of UniProt P0DTC2
Elsewhere: RCSB PDB 7KZB · PDBe 7KZB · UniProt P0DTC2

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