Research workbench

Structure of the SARS-cov-2 rbd in complex with neutralizing antibody C099 and CR3022

Analyse Structure of the SARS-cov-2 rbd in complex with neutralizing antibody C099 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7R8L
Type: protein
Length: 1,064 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: C099 Fab heavy chain; C099 Fab light chain; Spike protein S1; CR3022 Fab heavy chain…
UniProt: P0DTC2
Ligands: NAG, BMA, FUC
Pockets: 15 · best druggability 0.59

Structure

x-ray diffraction · 5 distinct chains · 9% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	C099 Fab heavy chain	protein	214	8% helix, 53% strand	—
L	C099 Fab light chain	protein	213	8% helix, 51% strand	—
E	Spike protein S1	protein	194	15% helix, 30% strand	P0DTC2
C	CR3022 Fab heavy chain	protein	222	7% helix, 52% strand	—
D	CR3022 Fab light chain	protein	221	6% helix, 51% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E
BMA · beta-D-mannopyranose · sugar
FUC · alpha-L-fucopyranose · sugar · chains E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	62	0.59	0.91	19	empty
2	395	0.55	0.74	47	empty
3	197	0.53	0.78	28	empty
4	300	0.53	0.75	44	empty
5	128	0.47	0.78	16	empty

Interfaces

6 interfaces between chains.

C–D · 2014 Å² buried · 16 hydrogen bonds · protein-protein
H–L · 1749 Å² buried · 16 hydrogen bonds · protein-protein
H–E · 783 Å² buried · 13 hydrogen bonds · protein-protein
E–C · 620 Å² buried · 10 hydrogen bonds · protein-protein
L–E · 459 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

7R8L · Structure of the SARS-CoV-2 RBD in complex with neutralizing antibody C099 and CR3022 · 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 7R8L · PDBe 7R8L · UniProt P0DTC2

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.