Proteins and Virion

Viral/Host Proteins and the Virion itself

Virus (SARS-CoV-2 and SARS-CoV), and Host based proteins are referenced here as well as the whole virion particle.

Data classification:
  • Structures: Data defining structures determined by experimental methods and referenced via a unique identifier such as a PDB ID.
  • Models: Derived, integrated, or refined structures from multiple data sources prepared for different computational tasks.
  • Simulations: The datasets produced as a result of applying the models to different scientific techniques.
ZhangPLpro-nsp33CLpro-nsp5nsp7nsp9RdRPnsp1nsp2nsp4nsp6nsp8nsp10spikeHelicaseVirionVirionVirionNucleoproteinOpen Reading Frame 7a

Virion Particle

SARS-CoV-2 Virion

The complete virion particle consisting of all proteins and interactions in the Viral categories

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Coarse Grained SARS-CoV-2 Virion

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Viral Proteins

Viral Spike Proteins

Viral Spike Fusion Core

Fusion core of the spike’s S2 stalk. Includes the Heptad Repeats, HR1 and HR2
Peptide
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[6lxt] Structure of Post Fusion Core of 2019-NCoV S2 Subunit
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SARS-CoV-2 Spike (S) glycoprotein

The external glyocoprotein of the virus envelope required for fusion and entry into human host cells.

Small Molecule Peptide Antiviral
Top Structural Data: [See All]
[6VSB] Prefusion 2019-NCoV Spike Glycoprotein With a Single Receptor-Binding Domain Up
[7jx3] Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology
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Ab 6D3 Bound to SARS-CoV-2 Spike in One RBD Up State

Spike by Yang Zhang Lab

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MD simulations of trimeric SARS-Cov2 spike protein ectodomain in explicit solvent. Data were collected for apo, linoleic acid bound and other putative ligands (3x200 ns in each case)

DESRES-ANTON-10897850 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein, no water or ions


Viral Protease, Polymerase, and Nonstructured Proteins

SARS-CoV-2 main protease (3CLpro or NSP5)

Cysteine protease essential for viral maturation

Small Molecule
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[6LU7] The Crystal Structure of COVID-19 Main Protease in Complex With an Inhibitor N3
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Coarse Grained 6y2g (PDB 6Y2G)

SARS-CoV-2 Dimeric Main Protease Without Ligand Based on PDB 6LU7

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Simulation files for docking a small molecule inhibitor (X77) to an Mpro target using NarupaIMD

AMOEBA 15.14 microsecond trajectory of Main Protease


SARS-CoV-2 Macrodomain (NSP3)

Macrodomain (NSP3, Macrodomain, or X) is a viral protein that is believed to be involved in repressing host immune response from its ability to remove ADP-ribose from ADP-ribosylated proteins and RNA.
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SIRAH-CoV2 initiative - Apo ADP-ribose phosphatase of NSP3

Folding@home simulations of nsp3 macrodomain


SARS-CoV-2 Papain-like protease (NSP3)

PLpro (NSP3, papain-like protease) is a viral cysteine protease responsible for maturation of the viral polyprotein, necessary for infection. Also involved in repressing host immune response.

Small Molecule
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[6W02] Crystal Structure of ADP Ribose Phosphatase of NSP3 From SARS CoV-2 in the Complex With ADP Ribose
[4ow0] X-Ray Structural and Biological Evaluation of a Series of Potent and Highly Selective Inhibitors of Human Coronavirus Papain-Like Proteases
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Refinement of AplhaFold PLpro C Terminal by FeigLab

Refinement of PLpro by FeigLab

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SIRAH-CoV2 initiative - Papain-like Protease

Apo SARS-CoV-2 PLPro (from PDB 6W9C C-chain)


SARS-CoV-2 RNA Polymerase (NSP12)

RNA-dependent, RNA polymerase.
Antiviral Small Molecule
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[7BV2] The Nsp12-Nsp7-Nsp8 Complex Bound to the Template-Primer RNA and Triphosphate Form of Remdesivir(RTP)
[7BTF] SARS-CoV-2 RNA-Dependent RNA Polymerase in Complex With Cofactors in Reduced Condition
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SARS-CoV-2 RdRp Complex (Nsp12+2*nsp8+nsp7) + RNA Template-Primer + RTP (Remdesivir Tri-Phosphate) Model for MD Simulations

Docking-Based Repurposing Study of Approved Drugs Against Truncated RdRp

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DESRES-ANTON-10917618 10 µs simulation of SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex, no water or zinc

Gromacs 100 ns MD of SARS-CoV-2 RdRp + RNA template-primer + RTP (Remdesivir Tri-Phosphate) model, All Atom model


Helicase coronavirus nonstructural protein 13 (NSP13)

The NSP13 SARS sequence is conserved and helicase activity is necessary for COVID replication. Helicase inhibition has been used for virus (HSV-amenavir) and cancer treatment (eIF41, RocA rocaglamides) and has gained interested in a potential disrupting target.
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[6ZSL] Crystal Structure of the SARS-CoV-2 Helicase at 1.94 Angstrom Resolution
[6ZB5] SARS CoV-2 Spike Protein, Closed Conformation, C3 Symmetry
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SWISS-MODEL Helicase

Helicase (NSP13) by Yang Zhang Lab

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SIRAH-CoV2 initiative - Helicase

Folding@home simulations of nsp13


Coronavirus nonstructural protein 1

Suppressor of host genome expression
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Refinement of SWISS-MODEL Nsp1 by FeigLab

NSP1 by Yang Zhang Lab

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Coronavirus nonstructural protein 10

Suppressor of host genome expression
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[6W4H] 1.80 Angstrom Resolution Crystal Structure of NSP16 - NSP10 Complex From SARS-CoV-2
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Nsp14_rna_dry_segname_psf

Nsp14_nsp10_dry_segname_psf

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Amber Trajectories of NSP14-NSP10 complex.

SIRAH-CoV2 initiative - NSP16 - NSP10 Complex


Coronavirus nonstructural protein 11

Suppressor of host genome expression
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Coronavirus nonstructural protein 14

Suppressor of host genome expression
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Nsp14_dry_segname_psf

SWISS-MODEL NSP10 + NSP14

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Amber Trajectories of NSP14-NSP10-RNA complex.

NAMD Trajectories of NSP14-NSP10-RNA complex.


Coronavirus nonstructural protein 15

Suppressor of host genome expression
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[6W01] The 1.9 a Crystal Structure of NSP15 Endoribonuclease From SARS CoV-2 in the Complex With a Citrate
[6M03] The Crystal Structure of COVID-19 Main Protease in Apo Form
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SWISS-MODEL NSP15

NSP15 by Yang Zhang Lab

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SIRAH-CoV2 initiative - NSP15 Endonuclease


Coronavirus nonstructural protein 16

Suppressor of host genome expression
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[6W4H] 1.80 Angstrom Resolution Crystal Structure of NSP16 - NSP10 Complex From SARS-CoV-2
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NSP16 by Yang Zhang Lab

SWISS-MODEL NSP10 + NSP16

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SIRAH-CoV2 initiative - NSP16 - NSP10 Complex


Coronavirus nonstructural protein 2

Suppressor of host genome expression
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Refinement of Nsp2 by FeigLab

Refinement of AplhaFold Nsp2 by FeigLab

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Coronavirus nonstructural protein 4

Suppressor of host genome expression
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Refinement of AplhaFold Nsp4 by FeigLab

Refinement of RaptorX Nsp4 by FeigLab

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Coronavirus nonstructural protein 6

Suppressor of host genome expression
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NSP6 by Yang Zhang Lab

Refinement of NSP6 in Membrane Environment by FeigLab

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Coronavirus nonstructural protein 7

Suppressor of host genome expression
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[6m71] SARS-Cov-2 RNA-Dependent RNA Polymerase in Complex With Cofactors
[7BTF] SARS-CoV-2 RNA-Dependent RNA Polymerase in Complex With Cofactors in Reduced Condition
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SARS-CoV-2 RdRp Complex (Nsp12+2*nsp8+nsp7) + RNA Template-Primer + RTP (Remdesivir Tri-Phosphate) Model for MD Simulations

NSP7 by Yang Zhang Lab

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Folding@home simulations of nsp7

SIRAH-CoV2 initiative - NSP7-NSP8 complex


Coronavirus nonstructural protein 8

Suppressor of host genome expression
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[7BV1] Cryo-EM Structure of the Apo Nsp12-Nsp7-Nsp8 Complex
[6YHU] Crystal Structure of the Nsp7-Nsp8 Complex of SARS-CoV-2
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SWISS-MODEL NSP7 + NSP8

Coarse Grained RNA-Dependent RNA Polymerase (PDB 6M71)

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SIRAH-CoV2 initiative - NSP7-NSP8 complex

Folding@home simulations of nsp8


Coronavirus nonstructural protein 9

Suppressor of host genome expression
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[6W4B] The Crystal Structure of Nsp9 RNA Binding Protein of SARS CoV-2
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NSP9 by Yang Zhang Lab

SWISS-MODEL NSP9

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Folding@home simulations of nsp9

SIRAH-CoV2 initiative - NSP9 RNA binding protein


Viral Open Reading Frame Proteins

Coronavirus Open Reading Frame 10

Behaviour of this protein is uncertain/unclear.
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ORF10 by Yang Zhang Lab

Refinement of RaptorX ORF10 by FeigLab

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Coronavirus Open Reading Frame 3a

Forms homotetrameric potassium sensitive ion channels and may modulate virus release.
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[6XDC] Cryo-EM Structure of SARS-CoV-2 ORF3a
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Refinement of AplhaFold ORF3a by FeigLab

Refinement of RaptorX ORF3a by FeigLab

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SIRAH-CoV2 initiative - Membrane embedded ORF3a


Coronavirus Open Reading Frame 6

Possible determinant of virus virulence.
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Refinement of RaptorX ORF6 by FeigLab

ORF6 by Yang Zhang Lab

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Coronavirus Open Reading Frame 7a

Non-structural protein which is dispensable for virus replication in cell culture. May suppress small interfering RNA (siRNA). May bind to host ITGAL, thereby playing a role in attachment or modulation of leukocytes.
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[6W37] STRUCTURE of the SARS-CoV-2 ORF7A ENCODED ACCESSORY PROTEIN
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Refinement of ORF7a by FeigLab

Refinement of SWISS-MODEL ORF7a by FeigLab

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SIRAH-CoV2 initiative - ORF7A enconded accessory protein


Coronavirus Open Reading Frame 7b

Behaviour of this protein is uncertain/unclear.
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Refinement of RaptorX ORF7b by FeigLab

Refinement of ORF7b by FeigLab

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Coronavirus Open Reading Frame 8

Behaviour of this protein is uncertain/unclear.
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Refinement of SWISS-MODEL ORF8 by FeigLab

Refinement of RaptorX ORF8 by FeigLab

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Viral Membrane Proteins

Membrane Glycoprotein

Viral envelope component that plays a role in morphogenesis.
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M Protein by Yang Zhang Lab

Refinement of M_protein by FeigLab

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Elucidation of SARS-Cov-2 Budding Mechanisms through Molecular Dynamics Simulations of M and E Protein Complexes


Viral Envelope Proteins

Envelope small membrane protein

Plays a central role in virus morphogenesis and assembly. Acts as a viroporin and self-assembles in host membranes forming pentameric protein-lipid pores that allow ion transport. Also plays a role in the induction of apoptosis.
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Refinement of E Protein in Membrane Environment by FeigLab

E Protein by Yang Zhang Lab

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Elucidation of SARS-Cov-2 Budding Mechanisms through Molecular Dynamics Simulations of M and E Protein Complexes

Coarse-grained molecular dynamics simulations of SARS-CoV-2 envelope protein E in the pentameric form


Viral Nucleocapsid Proteins

Nucleoprotein

Packages the positive strand viral genome RNA into a helical ribonucleocapsid (RNP) and plays a fundamental role during virion assembly through its interactions with the viral genome and membrane protein M. Plays an important role in enhancing the efficiency of subgenomic viral RNA transcription as well as viral replication.
Top Structural Data: [See All]
[6VYO] Crystal Structure of RNA Binding Domain of Nucleocapsid Phosphoprotein From SARS Coronavirus 2
[6M3M] Crystal Structure of SARS-CoV-2 Nucleocapsid Protein N-Terminal RNA Binding Domain
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SWISS-MODEL N Protein

N Protein by Yang Zhang Lab

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SIRAH-CoV2 initiative - Nucleocapsid protein N-terminal RNA binding domain

SIRAH-CoV2 initiative - RNA binding domain of nucleocapsid phosphoprotein



Host Proteins

Angiotensin-converting enzyme 2 (ACE2)

Extracellular carboxypeptidase expressed in lung tissue that is the host receptor for SARS-CoV-2 viral fusion.
Small Molecule Antiviral
Top Structural Data: [See All]
[6m0j] Crystal Structure of SARS-CoV-2 Spike Receptor-Binding Domain Bound With ACE2
[1R4L] Inhibitor Bound Human Angiotensin Converting Enzyme-Related Carboxypeptidase (ACE2)
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Structure of SARS Coronavirus Spike Receptor-Binding Domain Complexed With Its Receptor in Aqueous Solution

UK Variant SARS-CoV-2 Spike RBD-ACE2 Complex With 1 Salt Bridge

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A 10 µs simulation of a SARS-CoV-1 and SARS-CoV-2 chimera-ACE2 complex, no water or ions

Folding@home simulations of the SARS-CoV-2 spike RBD bound to human ACE2


Sodium Dependent Neutral Amnio Acid Transporter (BoAT1)

Chaperoned by ACE2 during S1 binding
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[6m17] The 2019-NCoV RBD/ACE2-B0AT1 Complex
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SARS-CoV-2 RBD/ACE2-B0AT1 Complex in Aqueous Solution

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DESRES-ANTON-10905033 10 µs simulation of the SARS-CoV-2-ACE2 complex, no water or ions

DESRES-ANTON-10905033 10 µs simulation of the SARS-CoV-2-ACE2 complex in aqueous solution


Ab Receptor in Host Cells (FcR)

Polymeric immunoglobulin receptor
Antibody Antiviral Peptide Immunotherapy
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Furin / PACE

Furin or PACE protein
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Furin Bound to SARS-CoV-2 Spike in One RBD Up State

Furin Bound to Delta Variant SARS-CoV-2 Spike in One RBD Up State

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Interleukin-6 (IL-6) receptor

Inflammatory cytokines and chemokines, including interleukin-6 (IL-6), have been observed to be significantly elevated in COVID-19 patients with severe disease. Blockade of IL-6 signaling has been proposed as a therapeutic mechanism to prevent cytokine storm, also known as cytokine release syndrome (CRS).
Antibody
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Programmed cell death factor 1

Immune checkpoint that guards against autoimmunity
Antibody
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p38 Mitogen-Activated Protein Kinase (MPAK)

p38 kinase which activates in response to infections
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Transmembrane Protease Serine 2

Transmembrane serine protease which has been shown to be involved in spike protein cleavage.
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Homology Model of Human TMPRSS2

TMPRSS2 Bound to SARS-CoV-2 Spike in One RBD Up State

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