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- PDB-1cqq: TYPE 2 RHINOVIRUS 3C PROTEASE WITH AG7088 INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 1cqq
TitleTYPE 2 RHINOVIRUS 3C PROTEASE WITH AG7088 INHIBITOR
ComponentsTYPE 2 RHINOVIRUS 3C PROTEASE
KeywordsHYDROLASE / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / DNA replication / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / virion attachment to host cell / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain ...Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Trypsin-like serine proteases / Thrombin, subunit H / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Chem-AG7 / Genome polyprotein
Similarity search - Component
Biological speciesHuman rhinovirus 2
MethodX-RAY DIFFRACTION / Resolution: 1.85 Å
AuthorsMatthews, D. / Ferre, R.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Structure-assisted design of mechanism-based irreversible inhibitors of human rhinovirus 3C protease with potent antiviral activity against multiple rhinovirus serotypes.
Authors: Matthews, D.A. / Dragovich, P.S. / Webber, S.E. / Fuhrman, S.A. / Patick, A.K. / Zalman, L.S. / Hendrickson, T.F. / Love, R.A. / Prins, T.J. / Marakovits, J.T. / Zhou, R. / Tikhe, J. / Ford, ...Authors: Matthews, D.A. / Dragovich, P.S. / Webber, S.E. / Fuhrman, S.A. / Patick, A.K. / Zalman, L.S. / Hendrickson, T.F. / Love, R.A. / Prins, T.J. / Marakovits, J.T. / Zhou, R. / Tikhe, J. / Ford, C.E. / Meador, J.W. / Ferre, R.A. / Brown, E.L. / Binford, S.L. / Brothers, M.A. / DeLisle, D.M. / Worland, S.T.
History
DepositionAug 10, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / Item: _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYPE 2 RHINOVIRUS 3C PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5822
Polymers19,9821
Non-polymers6011
Water3,981221
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.3, 65.7, 77.9
Angle α, β, γ (deg.)90., 90., 90.
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TYPE 2 RHINOVIRUS 3C PROTEASE


Mass: 19981.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 2 / Genus: Rhinovirus / Species: Human rhinovirus ARhinovirus / References: UniProt: P04936
#2: Chemical ChemComp-AG7 / 4-{2-(4-FLUORO-BENZYL)-6-METHYL-5-[(5-METHYL-ISOXAZOLE-3-CARBONYL)-AMINO]-4-OXO-HEPTANOYLAMINO}-5-(2-OXO-PYRROLIDIN-3-YL)-PENTANOIC ACID ETHYL ESTER / RUPINTRIVIR, bound form / Rupintrivir


Mass: 600.678 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H41FN4O7 / Comment: antivirus, protease inhibitor*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG10K, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 13K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16.8 mg/mlprotein1drop
220 %(v/v)PEG100001reservoir
30.1 MHEPES1reservoir

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 8, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. all: 14527 / Num. obs: 13981 / % possible obs: 89.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.048 / Net I/σ(I): 10.3
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.231 / % possible all: 48.7
Reflection
*PLUS
Rmerge(I) obs: 0.019

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 1.85→10 Å / σ(F): 1.5 / σ(I): 1.5 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
all0.218 13981 -
Rfree-0 -
obs-12184 87.1 %
Refinement stepCycle: LAST / Resolution: 1.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1700 0 83 663 2446
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 1.5
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_deg2.9

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