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- PDB-4pie: Crystal structure of human adenovirus 2 protease a substrate base... -

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Basic information

Entry
Database: PDB / ID: 4pie
TitleCrystal structure of human adenovirus 2 protease a substrate based nitrile inhibitor
Components
  • Pre-protein VI
  • Protease
KeywordsHydrolase/Hydrolase inhibitor / Adenain / adenovirus / cofactor / pVIc / cysteine protease / 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 / host cell / viral capsid ...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 / host cell / 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-3FO / ACETATE ION / Protease / Pre-protein VI
Similarity search - Component
Biological speciesHuman adenovirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsMac Sweeney, A. / Grosche, P. / Ellis, D. / Combrink, C. / Erbel, C. / Hughes, N. / Sirockin, F. / Melkko, S. / Bernardi, A. / Ramage, P. ...Mac Sweeney, A. / Grosche, P. / Ellis, D. / Combrink, C. / Erbel, C. / 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 1.1Aug 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 / _software.name
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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.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_symmetry

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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)25,2937
Polymers24,4682
Non-polymers8255
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-54 kcal/mol
Surface area9260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.312, 44.437, 98.921
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#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 / pVI


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

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Non-polymers , 5 types, 38 molecules

#3: Chemical ChemComp-3FO / N-{(2S)-2-(3-chlorophenyl)-2-[(methylsulfonyl)amino]acetyl}-L-phenylalanyl-N-[(2Z)-2-iminoethyl]glycinamide


Type: peptide-like / Mass: 507.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H26ClN5O5S
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 1.86 Å3/Da / Density % sol: 33.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1mM peptide-nitrile inhibitor was added to the protein and incubated for 30 minutes. 0.8M lithium sulphate, 0.1 M sodium acetate, pH 4.6

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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: Dec 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→44.4 Å / Num. obs: 14072 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 34.286 Å2 / Rmerge F obs: 0.086 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.059 / Χ2: 1.028 / Net I/σ(I): 19.48 / Num. measured all: 89405
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
1.94-1.990.460.4074.576585102410210.44299.7
1.99-2.050.3760.3545.3665679919900.38499.9
2.05-2.10.3110.286.5462579689680.305100
2.1-2.170.2610.2347.4560199459450.254100
2.17-2.240.230.1948.5555819099080.21299.9
2.24-2.320.1710.16610.0957568858850.181100
2.32-2.410.1470.13912.0457898618610.15100
2.41-2.50.1190.11613.6753548088070.12699.9
2.5-2.620.0940.09815.9652928128120.107100
2.62-2.740.080.07519.1649057627620.082100
2.74-2.890.0670.06920.742997157150.075100
2.89-3.070.0480.05326.0544056866860.058100
3.07-3.280.0340.04531.7242186426420.049100
3.28-3.540.0280.0435.8939616166160.044100
3.54-3.880.0240.03540.3134465675670.038100
3.88-4.340.0190.0343.3428905215200.03399.8
4.34-5.010.0160.02649.2128834584580.029100
5.01-6.140.0180.0345.7124504014010.033100
6.14-8.680.0180.02645.1417193183180.029100
8.680.0120.02149.4710291911900.02399.5

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Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.5.0102refinement
PDB_EXTRACT3.14data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NLN

1nln


Resolution: 1.94→40.53 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.13 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2603 704 5 %RANDOM
Rwork0.2069 13368 --
obs0.2096 14072 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 79.75 Å2 / Biso mean: 31.634 Å2 / Biso min: 18.43 Å2
Baniso -1Baniso -2Baniso -3
1--2.49 Å20 Å20 Å2
2--5.01 Å20 Å2
3----2.52 Å2
Refinement stepCycle: final / Resolution: 1.94→40.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1685 0 49 33 1767
Biso mean--43.35 32.81 -
Num. residues----213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0211784
X-RAY DIFFRACTIONr_angle_refined_deg2.0491.9682417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1025211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.72822.68382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.29715279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0891514
X-RAY DIFFRACTIONr_chiral_restr0.1380.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211389
X-RAY DIFFRACTIONr_mcbond_it1.1131.51070
X-RAY DIFFRACTIONr_mcangle_it1.90321720
X-RAY DIFFRACTIONr_scbond_it3.2723714
X-RAY DIFFRACTIONr_scangle_it4.8294.5697
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 51 -
Rwork0.265 967 -
all-1018 -
obs--99.71 %

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