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

Top Structural Data: [See All]

---

Top Models: [See All]

Coarse Grained SARS-CoV-2 Virion

Top Simulations: [See All]


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
Top Structural Data: [See All]
[6lxt] Structure of Post Fusion Core of 2019-NCoV S2 Subunit
Top Models: [See All]

---

Top Simulations: [See All]

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]
[6m0j] Crystal Structure of SARS-CoV-2 Spike Receptor-Binding Domain Bound With ACE2
[6vyb] SARS-CoV-2 Spike Ectodomain Structure (Open State)
Top Models: [See All]

Spike_full-Length_closed_amarolab

SWISS-MODEL Spike

Top Simulations: [See All]

Gromacs 60 ns MD of SARS-CoV-2 spike trimer, All Atom model

Trajectories of full-length SPIKE protein in the Closed state.


Viral Protease, Polymerase, and Nonstructured Proteins

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

Cysteine protease essential for viral maturation

Small Molecule
Top Structural Data: [See All]
[6Y2G] Crystal Structure (Orthorhombic Form) of the Complex Resulting From the Reaction Between SARS-CoV-2 (2019-NCoV) Main Protease and Tert-Butyl (1-((S)-1-(((S)-4-(Benzylamino)-3,4-Dioxo-1-((S)-2-Oxopyrrolidin-3-Yl)butan-2-Yl)amino)-3-Cyclopropyl-1-Oxopropan-2-Yl)-2-Oxo-1,2-Dihydropyridin-3-Yl)carbamate (Alpha-Ketoamide 13b)
[6LU7] The Crystal Structure of COVID-19 Main Protease in Complex With an Inhibitor N3
Top Models: [See All]

3CLpro by Yang Zhang Lab

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

Top Simulations: [See All]

Riken BDR 10 Microsecond Trajectory Protein Snapshot every 1ns

Riken BDR 10 Microsecond Trajectory System Snapshot every 10ns


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
Top Structural Data: [See All]
[4ow0] X-Ray Structural and Biological Evaluation of a Series of Potent and Highly Selective Inhibitors of Human Coronavirus Papain-Like Proteases
[6W02] Crystal Structure of ADP Ribose Phosphatase of NSP3 From SARS CoV-2 in the Complex With ADP Ribose
Top Models: [See All]

Refinement of PLpro by FeigLab

SARS-CoV-1 Ligand-Bound (PDB 4OW0)

Top Simulations: [See All]

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

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


SARS-CoV-2 RNA Polymerase (NSP12)

RNA-dependent, RNA polymerase.
Antiviral Small Molecule
Top Structural Data: [See All]
[7BV2] The Nsp12-Nsp7-Nsp8 Complex Bound to the Template-Primer RNA and Triphosphate Form of Remdesivir(RTP)
[7BV1] Cryo-EM Structure of the Apo Nsp12-Nsp7-Nsp8 Complex
Top Models: [See All]

SARS-CoV RdRP (NSP12) in Complex With Cofactors NSP7 and NSP8: ISOLDE Refined Model

SARS-CoV-2 Nsp7-Nsp8-Nsp12 RNA Polymerase Complex in Aqueous Solution

Top Simulations: [See All]

DESRES-ANTON-10917618 10 µs simulation of SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex in aqueous solution

Gromacs 100 ns MD of SARS-CoV-2 RdRp + RNA template-primer + ATP 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.
Top Structural Data: [See All]

---

Top Models: [See All]

Helicase (NSP13) by Yang Zhang Lab

SWISS-MODEL Helicase

Top Simulations: [See All]

Coronavirus nonstructural protein 1

Suppressor of host genome expression
Top Structural Data: [See All]

---

Top Models: [See All]

Refinement of Nsp1 by FeigLab

Refinement of SWISS-MODEL Nsp1 by FeigLab

Top Simulations: [See All]

Coronavirus nonstructural protein 10

Suppressor of host genome expression
Top Structural Data: [See All]
[6W4H] 1.80 Angstrom Resolution Crystal Structure of NSP16 - NSP10 Complex From SARS-CoV-2
Top Models: [See All]

SWISS-MODEL NSP10

SWISS-MODEL NSP10 + NSP14

Top Simulations: [See All]

Coronavirus nonstructural protein 11

Suppressor of host genome expression
Top Structural Data: [See All]

---

Top Models: [See All]

---

Top Simulations: [See All]

Coronavirus nonstructural protein 14

Suppressor of host genome expression
Top Structural Data: [See All]

---

Top Models: [See All]

NSP14 by Yang Zhang Lab

SWISS-MODEL NSP10 + NSP14

Top Simulations: [See All]

Coronavirus nonstructural protein 15

Suppressor of host genome expression
Top Structural Data: [See All]
[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
Top Models: [See All]

SWISS-MODEL NSP15

NSP15 by Yang Zhang Lab

Top Simulations: [See All]

Coronavirus nonstructural protein 16

Suppressor of host genome expression
Top Structural Data: [See All]
[6W4H] 1.80 Angstrom Resolution Crystal Structure of NSP16 - NSP10 Complex From SARS-CoV-2
Top Models: [See All]

SWISS-MODEL NSP10 + NSP16

NSP16 by Yang Zhang Lab

Top Simulations: [See All]

Coronavirus nonstructural protein 2

Suppressor of host genome expression
Top Structural Data: [See All]

---

Top Models: [See All]

Refinement of Baker Nsp2 by FeigLab

NSP2 by Yang Zhang Lab

Top Simulations: [See All]

Coronavirus nonstructural protein 4

Suppressor of host genome expression
Top Structural Data: [See All]

---

Top Models: [See All]

NSP4 by Yang Zhang Lab

Refinement of Nsp4 by FeigLab

Top Simulations: [See All]

Coronavirus nonstructural protein 6

Suppressor of host genome expression
Top Structural Data: [See All]

---

Top Models: [See All]

Refinement of NSP6 in Membrane Environment by FeigLab

Refinement of RaptorX Nsp6 by FeigLab

Top Simulations: [See All]

Coronavirus nonstructural protein 7

Suppressor of host genome expression
Top Structural Data: [See All]
[7BV1] Cryo-EM Structure of the Apo Nsp12-Nsp7-Nsp8 Complex
[7BV2] The Nsp12-Nsp7-Nsp8 Complex Bound to the Template-Primer RNA and Triphosphate Form of Remdesivir(RTP)
Top Models: [See All]

SWISS-MODEL NSP7 + NSP8 + RdRP

SARS-CoV-2 RdRp Complex (Nsp12+2*nsp8+nsp7) + RNA Template-Primer + ATP Model for MD Simulations

Top Simulations: [See All]

Gromacs 100 ns MD of SARS-CoV-2 RdRp + RNA template-primer + ATP model, All Atom model

Gromacs 300 ns MD of SARS-CoV-2 apo-RdRp model, All Atom model


Coronavirus nonstructural protein 8

Suppressor of host genome expression
Top Structural Data: [See All]
[6m71] SARS-Cov-2 RNA-Dependent RNA Polymerase in Complex With Cofactors
[7BV1] Cryo-EM Structure of the Apo Nsp12-Nsp7-Nsp8 Complex
Top Models: [See All]

SARS-CoV RdRP (NSP12) in Complex With Cofactors NSP7 and NSP8: ISOLDE Refined Model

SARS-CoV-2 Nsp7-Nsp8-Nsp12 RNA Polymerase Complex in Aqueous Solution

Top Simulations: [See All]

Gromacs 100 ns MD of SARS-CoV-2 RdRp + RNA template-primer + ATP model, All Atom model

Gromacs 300 ns MD of SARS-CoV-2 apo-RdRp model, All Atom model


Coronavirus nonstructural protein 9

Suppressor of host genome expression
Top Structural Data: [See All]

---

Top Models: [See All]

NSP9 by Yang Zhang Lab

SWISS-MODEL NSP9

Top Simulations: [See All]

Viral Open Reading Frame Proteins

Coronavirus Open Reading Frame 10

Behaviour of this protein is uncertain/unclear.
Top Structural Data: [See All]

---

Top Models: [See All]

Refinement of RaptorX ORF10 by FeigLab

Refinement of ORF10 by FeigLab

Top Simulations: [See All]

Coronavirus Open Reading Frame 3a

Forms homotetrameric potassium sensitive ion channels and may modulate virus release.
Top Structural Data: [See All]

---

Top Models: [See All]

Refinement of RaptorX ORF3a by FeigLab

Refinement of AplhaFold ORF3a by FeigLab

Top Simulations: [See All]

Coronavirus Open Reading Frame 6

Possible determinant of virus virulence.
Top Structural Data: [See All]

---

Top Models: [See All]

ORF6 by Yang Zhang Lab

Refinement of ORF6 by FeigLab

Top Simulations: [See All]

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.
Top Structural Data: [See All]

---

Top Models: [See All]

ORF7a by Yang Zhang Lab

SWISS-MODEL Protein 7a

Top Simulations: [See All]

Coronavirus Open Reading Frame 7b

Behaviour of this protein is uncertain/unclear.
Top Structural Data: [See All]

---

Top Models: [See All]

Refinement of ORF7b by FeigLab

Refinement of RaptorX ORF7b by FeigLab

Top Simulations: [See All]

Coronavirus Open Reading Frame 8

Behaviour of this protein is uncertain/unclear.
Top Structural Data: [See All]

---

Top Models: [See All]

Refinement of SWISS-MODEL ORF8 by FeigLab

ORF8 by Yang Zhang Lab

Top Simulations: [See All]

Viral Membrane Proteins

Membrane Glycoprotein

Viral envelope component that plays a role in morphogenesis.
Top Structural Data: [See All]

---

Top Models: [See All]

Refinement of RaptorX M_protein by FeigLab

Refinement of M Protein in Membrane Environment by FeigLab

Top Simulations: [See All]

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.
Top Structural Data: [See All]

---

Top Models: [See All]

E Protein by Yang Zhang Lab

Refinement of E Protein in Membrane Environment by FeigLab

Top Simulations: [See All]

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]

---

Top Models: [See All]

SWISS-MODEL N Protein

N Protein by Yang Zhang Lab

Top Simulations: [See All]


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]
[2AJF] Structure of SARS Coronavirus Spike Receptor-Binding Domain Complexed With Its Receptor
[6m17] The 2019-NCoV RBD/ACE2-B0AT1 Complex
Top Models: [See All]

Human ACE2 Ectodomain in Aqueous Solution (Inhibitor-Bound Closed State)

SWISS-MODEL Spike + ACE2

Top Simulations: [See All]

A 10 µs simulation of a SARS-CoV-1 and SARS-CoV-2 chimera-ACE2 complex in aqueous solution

DESRES-ANTON-10918441 2 µs simulations of 78 FDA approved or investigational drug molecules binding to the ectodomain of human ACE2, no water or ions


Sodium Dependent Neutral Amnio Acid Transporter (BoAT1)

Chaperoned by ACE2 during S1 binding
Top Structural Data: [See All]
[6m17] The 2019-NCoV RBD/ACE2-B0AT1 Complex
Top Models: [See All]

SARS-CoV-2 RBD/ACE2-B0AT1 Complex in Aqueous Solution

Top Simulations: [See All]

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
Top Structural Data: [See All]

---

Top Models: [See All]

---

Top Simulations: [See All]

Furin / PACE

Furin or PACE protein
Top Structural Data: [See All]

---

Top Models: [See All]

---

Top Simulations: [See All]

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
Top Structural Data: [See All]

---

Top Models: [See All]

---

Top Simulations: [See All]

Programmed cell death factor 1

Immune checkpoint that guards against autoimmunity
Antibody
Top Structural Data: [See All]

---

Top Models: [See All]

---

Top Simulations: [See All]

p38 Mitogen-Activated Protein Kinase (MPAK)

p38 kinase which activates in response to infections
Top Structural Data: [See All]

---

Top Models: [See All]

---

Top Simulations: [See All]

Transmembrane Protease Serine 2

Transmembrane serine protease which has been shown to be involved in spike protein cleavage.
Top Structural Data: [See All]

---

Top Models: [See All]

TMPRSS2 Homology Model With Substrate Overlaid

TMPRSS2 Homology Model With Benzamidine Overlaid

Top Simulations: [See All]