MolNFT v1 · #169444 · protein

Crystal structure of SARS-cov-2 receptor binding domain in complex with neutralizing antibody CC12.3

6XC4 · Spike protein S1: “Crystal structure of SARS-cov-2 receptor binding domain in complex with neutralizing antibody CC12.3”. X-ray diffraction, 1 ligand (NAG), 11 pockets (best druggability 0.71). MolNFT v1 #169444 on GenesisL1: 3D…

PDB: 6XC4
Type: protein
Length: 1,253 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike protein S1; CC12.3 heavy chain; CC12.3 light chain
UniProt: P0DTC2
Ligands: NAG
Pockets: 11 · best druggability 0.71

Structure

x-ray diffraction · 5 distinct chains · 10% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike protein S1	protein	199	16% helix, 30% strand	P0DTC2
H	CC12.3 heavy chain	protein	220	6% helix, 52% strand	—
L, Y	CC12.3 light chain	protein	213	6% helix, 51% strand	—
Z	Spike protein S1	protein	194	18% helix, 30% strand	P0DTC2
X	CC12.3 heavy chain	protein	214	7% helix, 54% 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

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	570	0.71	0.79	67	empty
2	497	0.68	0.78	70	empty
3	276	0.60	0.79	38	empty
4	403	0.58	0.75	47	empty
5	371	0.56	0.74	57	empty

Interfaces

7 interfaces between chains.

H–L · 1768 Å² buried · 22 hydrogen bonds · protein-protein
X–Y · 1744 Å² buried · 19 hydrogen bonds · protein-protein
A–H · 738 Å² buried · 17 hydrogen bonds · protein-protein
Z–X · 737 Å² buried · 16 hydrogen bonds · protein-protein
A–Z · 260 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6XC4 · 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 6XC4 · PDBe 6XC4 · UniProt P0DTC2

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