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Crystal structure of the SARS-cov-2 rbd in complex with the human antibody CV2.2325

Analyse Crystal structure of the SARS-cov-2 rbd in complex with the human antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7QF0
Type: protein
Length: 625 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike protein S1; CV2.2325 heavy chain; CV2.2325 light chain
UniProt: P0DTC2
Ligands: NAG, NA, CL
Pockets: 4 · best druggability 0.53

Structure

x-ray diffraction · 3 distinct chains · 11% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike protein S1	protein	195	18% helix, 30% strand	P0DTC2
H	CV2.2325 heavy chain	protein	216	8% helix, 53% strand	—
L	CV2.2325 light chain	protein	214	6% helix, 50% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
NA · Sodium ion · metal · chains A
CL · Chloride ion · ion · 3 copies · chains H, L

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

Pockets

4 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	225	0.53	0.77	30	empty
2	319	0.53	0.74	39	empty
3	67	0.35	0.77	14	empty
4	98	0.33	0.73	17	empty

Interfaces

3 interfaces between chains.

H–L · 1933 Å² buried · 20 hydrogen bonds · protein-protein
A–H · 890 Å² buried · 21 hydrogen bonds · protein-protein
A–L · 563 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

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

Compared structures

7QF0 · Crystal structure of the SARS-CoV-2 RBD in complex with the human antibody CV2.2325 · 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 7QF0 · PDBe 7QF0 · UniProt P0DTC2

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