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- PDB-2yol: West Nile Virus NS2B-NS3 protease in complex with 3,4- dichloroph... -

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Basic information

Entry
Database: PDB / ID: 2yol
TitleWest Nile Virus NS2B-NS3 protease in complex with 3,4- dichlorophenylacetyl-Lys-Lys-GCMA
ComponentsSERINE PROTEASE SUBUNIT NS2B, SERINE PROTEASE NS3
KeywordsHYDROLASE / SERINE PROTEASE / INHIBITOR
Function / homology
Function and homology information


RNA 5'-cap (guanine-N7)-methylation / RNA stabilization / RNA folding chaperone / DNA/DNA annealing activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / RNA strand annealing activity / symbiont-mediated suppression of host apoptosis / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / positive regulation of viral genome replication ...RNA 5'-cap (guanine-N7)-methylation / RNA stabilization / RNA folding chaperone / DNA/DNA annealing activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / RNA strand annealing activity / symbiont-mediated suppression of host apoptosis / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / positive regulation of viral genome replication / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / protein-DNA complex / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral capsid / peptidase activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / protein dimerization activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / ribonucleoprotein complex / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / DNA binding / RNA binding / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Thrombin, subunit H - #120 / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / mRNA cap 0/1 methyltransferase / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C ...Thrombin, subunit H - #120 / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / mRNA cap 0/1 methyltransferase / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein M / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Trypsin-like serine proteases / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Thrombin, subunit H / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Chem-EBN / NICKEL (II) ION / Genome polyprotein
Similarity search - Component
Biological speciesWEST NILE VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHammamy, M.Z. / Haase, C. / Hammami, M. / Hilgenfeld, R. / Steinmetzer, T.
CitationJournal: Chemmedchem / Year: 2013
Title: Development and Characterization of New Peptidomimetic Inhibitors of the West Nile Virus Ns2B-Ns3 Protease.
Authors: Hammamy, M.Z. / Haase, C. / Hammami, M. / Hilgenfeld, R. / Steinmetzer, T.
History
DepositionOct 25, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE PROTEASE SUBUNIT NS2B, SERINE PROTEASE NS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3104
Polymers24,6021
Non-polymers7083
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.700, 118.700, 66.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein SERINE PROTEASE SUBUNIT NS2B, SERINE PROTEASE NS3 / FLAVIVIRIN PROTEASE NS2B REGULATORY SUBUNIT / NON-STRUCTURAL PROTEIN 2B / FLAVIVIRIN PROTEASE NS3 ...FLAVIVIRIN PROTEASE NS2B REGULATORY SUBUNIT / NON-STRUCTURAL PROTEIN 2B / FLAVIVIRIN PROTEASE NS3 CATALYTIC SUBUNIT / NON-STRUCTURAL PROTEIN 3


Mass: 24602.377 Da / Num. of mol.: 1 / Fragment: NS2B, RESIDUES 1420-1466,AND NS3,1502-1671
Source method: isolated from a genetically manipulated source
Details: RESIDUES SER47 TO PRO91 BELONG TO NS2B, WHICH WE DESIGNATED AS MOLECULE A IN THE ASSOCIATED PUBLICATION. RESIDUES GLY1002 TO GLU1169 (RESIDUE NUMBERS WERE INCREMENTED BY 1000) BELONG TO NS3, ...Details: RESIDUES SER47 TO PRO91 BELONG TO NS2B, WHICH WE DESIGNATED AS MOLECULE A IN THE ASSOCIATED PUBLICATION. RESIDUES GLY1002 TO GLU1169 (RESIDUE NUMBERS WERE INCREMENTED BY 1000) BELONG TO NS3, WHICH WE DESIGNATED AS MOLECULE B IN THE ASSOCIATED PUBLICATION.
Source: (gene. exp.) WEST NILE VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD
References: UniProt: P06935, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EBN / (S)-6-amino-N-((S)-6-amino-1-(((1r,4S)-4-guanidinocyclohexyl)methylamino)-1-oxohexan-2-yl)-2-(2-(3,4-dichlorophenyl)acetamido)hexanamide / 3,4-dichlorophenylacetyl-Lys-Lys-GCMA


Mass: 613.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H46Cl2N8O3
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 46-49 REMAINED FROM THE N-TERMINAL HIS TAG AFTER THROMBIN CLEAVAGE. RESIDUES 97-105 BELONG ...RESIDUES 46-49 REMAINED FROM THE N-TERMINAL HIS TAG AFTER THROMBIN CLEAVAGE. RESIDUES 97-105 BELONG TO THE ARTIFICIAL LINKER BETWEEN NS2B AND NS3

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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: 5.19 Å3/Da / Density % sol: 76.3 % / Description: NONE
Crystal growDetails: 20% (W/V) POLYETHYLENE GLYCOL (PEG)3350, 0.1 M HEPES, PH 7.4

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3.2→51.38 Å / Num. obs: 9157 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 9.7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 12.2
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FP7

2fp7


Resolution: 3.2→102.77 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.899 / SU B: 12.294 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.572 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20681 437 4.8 %RANDOM
Rwork0.18759 ---
obs0.18849 8685 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.529 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0.3 Å20 Å2
2---0.6 Å20 Å2
3---0.9 Å2
Refinement stepCycle: LAST / Resolution: 3.2→102.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 43 7 1679
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221721
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.9612333
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8185213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2332574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.88115278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.161157
X-RAY DIFFRACTIONr_chiral_restr0.0990.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211309
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6821.51050
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27521692
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3043671
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3424.5639
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 32 -
Rwork0.246 629 -
obs--100 %

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