7EK6: Viral peptides IPB19/N52

Structure of viral peptides IPB19/N52. Determined by X-ray diffraction at 1.24 Å resolution. Released 9 Jun 2021.

Method: X-ray diffraction
Resolution: 1.24 Å
Organism: Severe acute respiratory syndrome coronavirus 2
Chains: 2
Atoms: 753
Mol. weight: 9.91 kDa
Released: 9 Jun 2021

Explore 7EK6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7EK6 contains 3 α-helices and 0 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	909-956	48

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1180-1192	13
α-helix	1193-1196	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike protein S2	A	protein	52	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)
Spike protein S2	B	protein	37	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7EK6_1 Spike protein S2 (chains A)
FNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQ

Sequence of entity 2 (B), FASTA

>7EK6_2 Spike protein S2 (chains B)
SVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIK

Primary citation

Structure-based design and characterization of novel fusion-inhibitory lipopeptides against SARS-CoV-2 and emerging variants. Yu, D., Zhu, Y., Jiao, T. et al. Emerg Microbes Infect (2021) 10:1227-1240. DOI 10.1080/22221751.2021.1937329 · PubMed

Other PDB entries of the same protein (UniProt P0DTC2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Z8O 0.96 Å, Crystal structure of SARS-CoV-2 S RBD in complex with a stapled peptide
7Y8J 1.03 Å, 3D1 in complex with 6-mer HR1 peptide from SARS-CoV-2
9FC2 1.21 Å, The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the…
7EAM 1.4 Å, immune complex of SARS-CoV-2 RBD and cross-neutralizing antibody 7D6
7M53 1.4 Å, B6 Fab fragment bound to the SARS-CoV/SARS-CoV-2 spike stem helix peptide
8CMC 1.42 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530
7M8U 1.45 Å, Crystal Structure of HLA-B*35:01 in complex with IPFAMQMAY, an 9-mer epitope from…
7ZR2 1.45 Å, Crystal structure of a chimeric protein mimic of SARS-CoV-2 Spike HR1 in complex with HR2
8D36 1.45 Å, Crystal structure of SARS-CoV-2 fusion peptide in complex with neutralizing antibody…
8ENS 1.45 Å, Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 spike tail…
8ENW 1.45 Å, Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 clientized spike…
6M1V 1.5 Å, Crystal structure of post fusion core of 2019-nCoV S2 subunit

Browse structure collections

About this viewer

MolViewer shows 7EK6 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.