COVID-3D | Uridylate-specific endoribonuclease (NendoU)

3D Structure

Structure

APO

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RepresentationCartoon
Color Scheme info_outlineSecondary Structure
Pockets info_outline#1 - Volume 2853.376 Å³

                                                
                                                    Pocket info_outline
                                                
                                                    Surface info_outline
                                                
Fragment Hotspots info_outline:
                                                
                                                    Acceptor
                                                
                                                    Donor
                                                
                                                    Apolar

                                                
                                                    COVID-19 Variants info_outline
                                                
                                                    Variant Frequency info_outline
                                                
                                                    Evolutionary Coupling info_outline

Mutations from SARS

Mutations from Bat RaTG13

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Sequence

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Mutational Tolerance (Missense Tolerance Ratio)

Horizontal lines show gene-specific MTR percentiles 5th, 25th, 50th, and neutrality (MTR = 1.0)

Mutations Analysis Saturation Mutagenesis

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                                                    Residue Properties
                                                
                                                    Stability Scores
                                                
                                                    PSSM Scores
                                                
                                                    AAindex
                                                
                                                    Clade Frequency
                                                
                                                    Contacts

SARS-CoV2 Circulating Variants

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Position	AA from	AA to	Chain	Frequency (%)	Depth (Å)	Phi (°)	Psi (°)	RSA (%)	SST	MTR Score	Consurf Score	ΔAtomic Fluctuation (Å)	ΔEnergy Deformation (kcal/mol)	ΔΔG_mCSM^stability	ΔΔG_DynaMut^stability	ΔΔG_DUET^stability	ΔΔG_SDM^stability	ΔΔG_ENCoM^stability	ΔΔS_ENCoM^vib	Distance to PPI (Å)	PPI affinity	Hydrophobics	Positives	Negatives	Acceptors	Donnors	Aromatics	Sulfurs	Neutral	Details

Position	AA from	AA to	Chain	Frequency (%)	Depth (Å)	Phi (°)	Psi (°)	RSA (%)	SST	MTR Score	Consurf Score	ΔAtomic Fluctuation (Å)	ΔEnergy Deformation (kcal/mol)	ΔΔG_mCSM^stability	ΔΔG_DynaMut^stability	ΔΔG_DUET^stability	ΔΔG_SDM^stability	ΔΔG_ENCoM^stability	ΔΔS_ENCoM^vib	Distance to PPI (Å)	PPI affinity	Hydrophobics	Positives	Negatives	Acceptors	Donnors	Aromatics	Sulfurs	Neutral	Details
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Mutations from SARS

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Position	AA from	AA to	Chain	Frequency (%)	Depth (Å)	Phi (°)	Psi (°)	RSA (%)	SST	MTR Score	Consurf Score	ΔAtomic Fluctuation (Å)	ΔEnergy Deformation (kcal/mol)	ΔΔG_mCSM^stability	ΔΔG_DynaMut^stability	ΔΔG_DUET^stability	ΔΔG_SDM^stability	ΔΔG_ENCoM^stability	ΔΔS_ENCoM^vib	Distance to PPI (Å)	PPI affinity	Hydrophobics	Positives	Negatives	Acceptors	Donnors	Aromatics	Sulfurs	Neutral	Details

Position	AA from	AA to	Chain	Frequency (%)	Depth (Å)	Phi (°)	Psi (°)	RSA (%)	SST	MTR Score	Consurf Score	ΔAtomic Fluctuation (Å)	ΔEnergy Deformation (kcal/mol)	ΔΔG_mCSM^stability	ΔΔG_DynaMut^stability	ΔΔG_DUET^stability	ΔΔG_SDM^stability	ΔΔG_ENCoM^stability	ΔΔS_ENCoM^vib	Distance to PPI (Å)	PPI affinity	Hydrophobics	Positives	Negatives	Acceptors	Donnors	Aromatics	Sulfurs	Neutral	Details
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Mutations from Bat RaTG13

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Position	AA from	AA to	Chain	Frequency (%)	Depth (Å)	Phi (°)	Psi (°)	RSA (%)	SST	MTR Score	Consurf Score	ΔAtomic Fluctuation (Å)	ΔEnergy Deformation (kcal/mol)	ΔΔG_mCSM^stability	ΔΔG_DynaMut^stability	ΔΔG_DUET^stability	ΔΔG_SDM^stability	ΔΔG_ENCoM^stability	ΔΔS_ENCoM^vib	Distance to PPI (Å)	PPI affinity	Hydrophobics	Positives	Negatives	Acceptors	Donnors	Aromatics	Sulfurs	Neutral	Details

Position	AA from	AA to	Chain	Frequency (%)	Depth (Å)	Phi (°)	Psi (°)	RSA (%)	SST	MTR Score	Consurf Score	ΔAtomic Fluctuation (Å)	ΔEnergy Deformation (kcal/mol)	ΔΔG_mCSM^stability	ΔΔG_DynaMut^stability	ΔΔG_DUET^stability	ΔΔG_SDM^stability	ΔΔG_ENCoM^stability	ΔΔS_ENCoM^vib	Distance to PPI (Å)	PPI affinity	Hydrophobics	Positives	Negatives	Acceptors	Donnors	Aromatics	Sulfurs	Neutral	Details
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Normal Mode Analysis

                                            Porcupine Plots info_outline

Modes Visualisation info_outline

Deformation Energy info_outline
                                                
Atomic Fluctuation info_outline

Molecular Dynamics

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Protein Structure Mutations

Uridylate-specific endoribonuclease (NendoU) (Uniprot: P0DTD1 - GenBank: QHD43415_14)

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Mutational Tolerance (Missense Tolerance Ratio)

SARS-CoV2 Circulating Variants

Mutations from SARS info_outline

Mutations from Bat RaTG13 info_outline

Porcupine Plots info_outline

Modes Visualisation info_outline

Deformation Energy info_outline

Atomic Fluctuation info_outline

Mutations from SARS

Mutations from Bat RaTG13

Porcupine Plots

Modes Visualisation

Deformation Energy

Atomic Fluctuation