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Structure of SARS-cov-2 spike protein receptor binding domain in complex with a potent neutralizing antibody, CV30 Fab

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

PDB: 6XE1
Type: protein
Length: 638 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CV30 Fab heavy chain; CV30 Fab kappa chain; Spike protein S1
UniProt: P0DTC2
Ligands: NAG
Pockets: 5 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 10% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	CV30 Fab heavy chain	protein	219	5% helix, 49% strand	—
L	CV30 Fab kappa chain	protein	212	8% helix, 54% strand	—
E	Spike protein S1	protein	207	16% helix, 27% strand	P0DTC2

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains E

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	265	0.73	0.87	26	empty
2	378	0.55	0.74	48	empty
3	83	0.40	0.78	20	empty
4	89	0.35	0.75	19	empty
5	52	0.30	0.76	12	empty

Interfaces

3 interfaces between chains.

H–L · 1769 Å² buried · 14 hydrogen bonds · protein-protein
H–E · 802 Å² buried · 21 hydrogen bonds · protein-protein
L–E · 322 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 2 modified, 1 glycan (disulfide, cyclization, N-glycosylation).

Compared structures

6XE1 · Structure of SARS-CoV-2 spike protein receptor binding domain in complex with a potent… · 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 6XE1 · PDBe 6XE1 · UniProt P0DTC2

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