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Crystal structure of SARS-cov-2 receptor binding domain in complex with neutralizing antibody CC12.1

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: 6XC2
Type: protein
Length: 1,246 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike protein S1; CC12.1 light chain; CC12.1 heavy chain
UniProt: P0DTC2
Ligands: NAG
Pockets: 12 · best druggability 0.70

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, Z	Spike protein S1	protein	193	17% helix, 28% strand	P0DTC2
L, Y	CC12.1 light chain	protein	215	6% helix, 52% strand	—
H, X	CC12.1 heavy chain	protein	215	5% helix, 50% strand	—

Ligands and binding sites

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

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

Pockets

12 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	763	0.70	0.77	63	empty
2	430	0.59	0.75	51	empty
3	391	0.57	0.74	48	empty
4	104	0.39	0.76	27	empty
5	94	0.37	0.75	18	empty

Interfaces

8 interfaces between chains.

L–H · 1870 Å² buried · 19 hydrogen bonds · protein-protein
Y–X · 1865 Å² buried · 17 hydrogen bonds · protein-protein
Z–X · 837 Å² buried · 18 hydrogen bonds · protein-protein
A–H · 836 Å² buried · 18 hydrogen bonds · protein-protein
Z–Y · 636 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

6XC2 · Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing… · 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 6XC2 · PDBe 6XC2 · UniProt P0DTC2

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