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Crystal structure of SARS-cov-2 receptor binding domain in complex with neutralizing antibody adi-55688

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: 7U2E
Type: protein
Length: 628 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike protein S1; Adi-55688 heavy chain; Adi-55688 light chain
UniProt: P0DTC2
Ligands: NAG, SO4
Pockets: 7 · best druggability 0.59

Structure

x-ray diffraction · 3 distinct chains · 10% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike protein S1	protein	194	14% helix, 28% strand	P0DTC2
H	Adi-55688 heavy chain	protein	219	9% helix, 48% strand	—
L	Adi-55688 light chain	protein	215	7% helix, 49% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
SO4 · Sulfate ion · ion · 9 copies · chains A, 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	526	0.59	0.73	59	SO4
2	201	0.50	0.76	27	SO4
3	103	0.39	0.75	24	empty
4	70	0.34	0.76	14	empty
5	71	0.33	0.75	14	empty

Interfaces

3 interfaces between chains.

H–L · 1764 Å² buried · 17 hydrogen bonds · protein-protein
A–H · 508 Å² buried · 8 hydrogen bonds · protein-protein
A–L · 221 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

7U2E · 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 7U2E · PDBe 7U2E · UniProt P0DTC2

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