Research workbench

Crystal structure of SARS-cov-2 receptor binding domain in complex with antibodies CC12.1 and CR3022

Analyse Crystal structure of SARS-cov-2 receptor binding domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6XC3
Type: protein
Length: 1,065 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CR3022 heavy chain; CR3022 light chain; CC12.1 light chain; CC12.1 heavy chain; Spike…
UniProt: P0DTC2
Ligands: NAG
Pockets: 15 · best druggability 0.59

Structure

x-ray diffraction · 5 distinct chains · 8% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	CR3022 heavy chain	protein	222	6% helix, 51% strand	—
L	CR3022 light chain	protein	221	5% helix, 52% strand	—
A	CC12.1 light chain	protein	215	6% helix, 51% strand	—
B	CC12.1 heavy chain	protein	214	6% helix, 52% strand	—
C	Spike protein S1	protein	193	17% helix, 28% strand	P0DTC2

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains C

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

Pockets

15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	418	0.59	0.75	52	empty
2	184	0.56	0.80	31	empty
3	284	0.52	0.75	46	empty
4	174	0.48	0.76	26	empty
5	182	0.44	0.74	29	empty

Interfaces

6 interfaces between chains.

H–L · 1895 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1822 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 778 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 626 Å² buried · 12 hydrogen bonds · protein-protein
H–C · 618 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6XC3 · Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies CC12.1… · 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 6XC3 · PDBe 6XC3 · UniProt P0DTC2

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