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Crystallographic structure of two neutralizing antibodies in complex with SARS-cov-2 spike receptor-binding domain (rbd)

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PDB: 7FCP
Type: protein
Length: 1,069 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike protein S1; P14-44 antibody Fab fragment heavy chain; P14-44 antibody Fab fragment…
UniProt: P0DTC2
Ligands: NAG
Pockets: 15 · best druggability 0.61

Structure

x-ray diffraction · 5 distinct chains · 9% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike protein S1	protein	185	16% helix, 30% strand	P0DTC2
H	P14-44 antibody Fab fragment heavy chain	protein	232	10% helix, 51% strand	—
L	P14-44 antibody Fab fragment light chain	protein	215	6% helix, 49% strand	—
B	P5-22 antibody Fab fragment heavy chain	protein	223	8% helix, 48% strand	—
D	P5-22 antibody Fab fragment light chain	protein	214	6% helix, 50% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
GOL · Glycerol · additive · 2 copies · chains H, B, D
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A

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

Pockets

15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	509	0.61	0.74	66	empty
2	497	0.59	0.74	55	empty
3	432	0.58	0.75	47	empty
4	186	0.57	0.81	32	TRS
5	236	0.55	0.78	38	empty

Interfaces

9 interfaces between chains.

H–L · 1919 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 1840 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 847 Å² buried · 9 hydrogen bonds · protein-protein
A–H · 748 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 253 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

7FCP · Crystallographic structure of two neutralizing antibodies in complex with SARS-CoV-2… · 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 7FCP · PDBe 7FCP · UniProt P0DTC2

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