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- PDB-4pid: Crystal structure of human adenovirus 2 protease with a weak pyri... -

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Basic information

Entry
Database: PDB / ID: 4pid
TitleCrystal structure of human adenovirus 2 protease with a weak pyrimidine nitrile inhibitor
Components
  • Pre-protein VI
  • Protease
KeywordsHydrolase/Hydrolase Inhibitor / Adenain / cysteine protease / adenovirus / pVIc cofactor / virus maturation / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


nuclear capsid assembly / adenain / lysis of host organelle involved in viral entry into host cell / viral procapsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / cysteine-type peptidase activity / virion component / viral capsid / host cell cytoplasm ...nuclear capsid assembly / adenain / lysis of host organelle involved in viral entry into host cell / viral procapsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / cysteine-type peptidase activity / virion component / viral capsid / host cell cytoplasm / cysteine-type endopeptidase activity / host cell nucleus / proteolysis / DNA binding
Similarity search - Function
Peptidase C5, adenain / Adenovirus endoprotease / Minor capsid protein VI / Minor capsid protein VI / Adenoviral Proteinase; Chain / Adenoviral Proteinase; Chain A / Papain-like cysteine peptidase superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2UQ / ACETATE ION / Protease / Pre-protein VI
Similarity search - Component
Biological speciesHuman adenovirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsMac Sweeney, A. / Grosche, P. / Ellis, D. / Combrink, K. / Erbel, P. / Hughes, N. / Sirockin, F. / Melkko, S. / Bernardi, A. / Ramage, P. ...Mac Sweeney, A. / Grosche, P. / Ellis, D. / Combrink, K. / Erbel, P. / Hughes, N. / Sirockin, F. / Melkko, S. / Bernardi, A. / Ramage, P. / Jarousse, N. / Altmann, E.
CitationJournal: Acs Med.Chem.Lett. / Year: 2014
Title: Discovery and structure-based optimization of adenain inhibitors.
Authors: Mac Sweeney, A. / Grosche, P. / Ellis, D. / Combrink, K. / Erbel, P. / Hughes, N. / Sirockin, F. / Melkko, S. / Bernardi, A. / Ramage, P. / Jarousse, N. / Altmann, E.
History
DepositionMay 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease
B: Pre-protein VI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7674
Polymers24,4682
Non-polymers2992
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-6 kcal/mol
Surface area10030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.783, 112.783, 50.347
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Protease / / Adenain / Adenovirus protease / AVP / Adenovirus proteinase / Endoprotease


Mass: 23114.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 2 / Gene: L3 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03252, adenain
#2: Protein/peptide Pre-protein VI / Protease cofactor / pVI-C


Mass: 1353.640 Da / Num. of mol.: 1 / Fragment: UNP residues 240-250 / Source method: obtained synthetically / Source: (synth.) Human adenovirus 2 / References: UniProt: P03274
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-2UQ / N-benzyl-2-[(Z)-iminomethyl]pyrimidine-5-carboxamide


Mass: 240.261 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12N4O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 3.78 Å3/Da / Density % sol: 67.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.8 M sodium/potassium tartrate, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.59→97.7 Å / Num. obs: 49317 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 24.337 Å2 / Rmerge F obs: 0.059 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.066 / Χ2: 1.009 / Net I/σ(I): 22.95 / Num. measured all: 495405
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.59-1.630.3430.5424.2836696363036300.571100
1.63-1.680.2740.4365.2135188353635360.46100
1.68-1.720.2280.3616.132293343234310.382100
1.72-1.780.1790.2937.6433202334633460.309100
1.78-1.840.1320.2329.8433613322132210.244100
1.84-1.90.1080.18811.9932793315231520.198100
1.9-1.970.0860.15314.6431129301130110.161100
1.97-2.050.0680.12217.9429702290929090.128100
2.05-2.140.0540.09721.7627190280628060.102100
2.14-2.250.0450.08424.7925958268026800.089100
2.25-2.370.0350.07329.1727078254425440.077100
2.37-2.510.0330.06731.8725383241824180.07100
2.51-2.690.0250.05637.2523584228222820.059100
2.69-2.90.0250.05140.1221041210421040.054100
2.9-3.180.0220.04543.3117534193519350.048100
3.18-3.560.0160.03951.2118138178617860.041100
3.56-4.110.0140.03657.3216048155615560.038100
4.11-5.030.0130.03358.813212133613360.035100
5.03-7.110.0140.03454.769502104010400.036100
7.110.0110.02962.8661215955940.0399.8

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Processing

Software
NameVersionClassification
XSCALEJan 30, 2009data scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NLN

1nln


Resolution: 1.59→48.84 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.973 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1892 2466 5 %RANDOM
Rwork0.1648 46850 --
obs0.1661 49316 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 58.91 Å2 / Biso mean: 18.571 Å2 / Biso min: 5.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.59→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1715 0 22 152 1889
Biso mean--39.28 27.8 -
Num. residues----215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.0221819
X-RAY DIFFRACTIONr_angle_refined_deg2.7861.9542464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2325223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76522.64487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18115301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6931516
X-RAY DIFFRACTIONr_chiral_restr0.210.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211429
X-RAY DIFFRACTIONr_mcbond_it1.7231.51096
X-RAY DIFFRACTIONr_mcangle_it2.92821771
X-RAY DIFFRACTIONr_scbond_it4.3023723
X-RAY DIFFRACTIONr_scangle_it6.6454.5688
LS refinement shellResolution: 1.59→1.631 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 181 -
Rwork0.23 3445 -
all-3626 -
obs--100 %

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