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Crystal structure of SARS-cov receptor binding domain in complex with human antibody CR3022

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

PDB: 7JN5
Type: protein
Length: 620 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CR3022 heavy chain; CR3022 light chain; Spike glycoprotein
UniProt: Q19QX0
Ligands: NAG, PO4
Pockets: 7 · best druggability 0.52

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	CR3022 heavy chain	protein	221	5% helix, 52% strand	—
L	CR3022 light chain	protein	220	6% helix, 52% strand	—
F	Spike glycoprotein	protein	179	16% helix, 27% strand	Q19QX0

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains H, F
PO4 · Phosphate ion · ion · chains H, L

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	316	0.52	0.74	41	empty
2	176	0.50	0.77	28	empty
3	108	0.50	0.81	25	empty
4	70	0.32	0.75	17	empty
5	74	0.32	0.74	13	empty

Interfaces

3 interfaces between chains.

H–L · 2016 Å² buried · 17 hydrogen bonds · protein-protein
H–F · 708 Å² buried · 12 hydrogen bonds · protein-protein
L–F · 330 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

7JN5 · Crystal structure of SARS-CoV receptor binding domain in complex with human antibody… · 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 Q19QX0
Elsewhere: RCSB PDB 7JN5 · PDBe 7JN5 · UniProt Q19QX0

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