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- PDB-4pis: Crystal structure of human adenovirus 8 protease in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4pis
TitleCrystal structure of human adenovirus 8 protease in complex with a nitrile inhibitor
Components
  • PVI
  • Protease
KeywordsHydrolase/Hydrolase inhibitor / adenain / cysteine protease / pVIc / cofactor / nitrile inhibitor / Hydrolase-Hydrolase inhibitor complex
Function / homology
Function and homology information


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 / virion component / viral capsid / host cell / host cell cytoplasm / cysteine-type endopeptidase activity ...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 / virion component / viral capsid / host cell / 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-3FU / Pre-protein VI / Protease
Similarity search - Component
Biological speciesHuman adenovirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 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 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen ...diffrn_detector / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_detector.detector / _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_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease
B: PVI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8433
Polymers24,3642
Non-polymers4791
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-5 kcal/mol
Surface area9650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.061, 42.061, 193.238
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Protease


Mass: 22993.312 Da / Num. of mol.: 1 / Fragment: UNP residues 2-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 8 / Gene: L3 / Production host: Escherichia coli (E. coli) / References: UniProt: B9A5C1
#2: Protein/peptide PVI


Mass: 1370.691 Da / Num. of mol.: 1 / Fragment: UNP residues 223-233 / Source method: obtained synthetically / Source: (synth.) Human adenovirus 8 / References: UniProt: B9A5B9
#3: Chemical ChemComp-3FU / N~2~-[(2R)-2-(3,5-dichlorophenyl)-2-(dimethylamino)acetyl]-N-({2-[(Z)-iminomethyl]pyrimidin-4-yl}methyl)-L-isoleucinamide


Type: peptide-like / Mass: 479.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H28Cl2N6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.03 Å3/Da / Density % sol: 39.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2mM inhibitor added. Cocrystallization in 0.2M sodium citrate, 20% PEG3350

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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: Sep 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→36.43 Å / Num. obs: 12338 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 47.92 Å2 / Rmerge F obs: 0.077 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.083 / Χ2: 1.11 / Net I/σ(I): 15.23 / Num. measured all: 111800
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.1-2.150.4160.6163.0181798598590.651100
2.15-2.210.5220.6412.8884958988980.679100
2.21-2.280.8130.912.7765418177910.97296.8
2.28-2.350.2530.3455.2583148438430.364100
2.35-2.420.1750.2716.8777067857850.286100
2.42-2.510.1230.2168.5576807787780.229100
2.51-2.60.1020.1710.6271837617610.18100
2.6-2.710.0820.14912.6864017027010.15899.9
2.71-2.830.0710.12514.5164707067060.133100
2.83-2.970.0550.11118.4264396666660.118100
2.97-3.130.0470.09321.1858596296290.098100
3.13-3.320.0440.08723.2355556256250.093100
3.32-3.550.0370.07525.6846205585580.08100
3.55-3.830.0360.0726.445975585570.07599.8
3.83-4.20.0280.06130.1941824944940.065100
4.2-4.70.0250.05531.338044584580.058100
4.7-5.420.0240.05430.9631504014010.058100
5.42-6.640.0230.05131.2730783613610.054100
6.64-9.390.020.04332.1322752862860.046100
9.390.0160.03631.1112721821810.03999.5

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Processing

Software
NameVersionClassification
XDSdata reduction
PDB_EXTRACT3.14data extraction
XSCALEdata scaling
BUSTER2.11.5refinement
RefinementResolution: 2.1→36.43 Å / Cor.coef. Fo:Fc: 0.9411 / Cor.coef. Fo:Fc free: 0.9146 / SU R Cruickshank DPI: 0.286 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.303 / SU Rfree Blow DPI: 0.226 / SU Rfree Cruickshank DPI: 0.223
RfactorNum. reflection% reflectionSelection details
Rfree0.279 617 5 %RANDOM
Rwork0.2319 ---
obs0.2343 12338 99.77 %-
Displacement parametersBiso max: 125.72 Å2 / Biso mean: 46.09 Å2 / Biso min: 25.76 Å2
Baniso -1Baniso -2Baniso -3
1--2.2824 Å20 Å20 Å2
2---2.2824 Å20 Å2
3---4.5648 Å2
Refine analyzeLuzzati coordinate error obs: 0.401 Å
Refinement stepCycle: final / Resolution: 2.1→36.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1709 0 32 32 1773
Biso mean--59.11 41 -
Num. residues----215
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d637SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes36HARMONIC2
X-RAY DIFFRACTIONt_gen_planes277HARMONIC5
X-RAY DIFFRACTIONt_it1818HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion219SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2115SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1818HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2458HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.18
X-RAY DIFFRACTIONt_other_torsion17.17
LS refinement shellResolution: 2.1→2.3 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.4324 141 4.99 %
Rwork0.3367 2687 -
all0.3414 2828 -
obs--99.77 %

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