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A SARS-cov-2 neutralizing antibody

Analyse A SARS-cov-2 neutralizing antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7F12
Type: protein
Length: 399 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike protein S1; Antibody
UniProt: P0DTC2
Ligands: NAG
Pockets: 5 · best druggability 0.51

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike protein S1	protein	169	16% helix, 28% strand	P0DTC2
B	Antibody	protein	230	4% helix, 50% strand	—

Ligands and binding sites

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

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

Pockets

5 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	178	0.51	0.78	25	empty
2	62	0.34	0.77	16	empty
3	85	0.33	0.74	23	empty
4	62	0.32	0.75	15	empty
5	52	0.30	0.76	11	empty

Interfaces

1 interface between chains.

A–B · 600 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

7F12 · A SARS-CoV-2 neutralizing antibody · 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 7F12 · PDBe 7F12 · UniProt P0DTC2

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