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- PDB-4wx6: Crystal structure of human adenovirus 8 protease with an irrevers... -

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Basic information

Entry
Database: PDB / ID: 4wx6
TitleCrystal structure of human adenovirus 8 protease with an irreversible vinyl sulfone inhibitor
Components
  • PVI
  • Protease
KeywordsHYDROLASE / cysteine protease / deubiquitinase / inhibitor
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-3VK / Protease / Pre-protein VI
Similarity search - Component
Biological speciesHuman adenovirus D serotype 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsGrosche, P. / Sirockin, F. / Mac Sweeney, A. / Ramage, P. / Erbel, P. / Melkko, S. / Bernardi, A. / Hughes, N. / Ellis, D. / Combrink, K. ...Grosche, P. / Sirockin, F. / Mac Sweeney, A. / Ramage, P. / Erbel, P. / Melkko, S. / Bernardi, A. / Hughes, N. / Ellis, D. / Combrink, K. / Jarousse, N. / Altmann, E.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2015
Title: Structure-based design and optimization of potent inhibitors of the adenoviral protease.
Authors: Grosche, P. / Sirockin, F. / Mac Sweeney, A. / Ramage, P. / Erbel, P. / Melkko, S. / Bernardi, A. / Hughes, N. / Ellis, D. / Combrink, K.D. / Jarousse, N. / Altmann, E.
History
DepositionNov 13, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease
B: PVI
C: Protease
D: PVI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8036
Polymers48,7284
Non-polymers1,0752
Water50428
1
A: Protease
B: PVI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9023
Polymers24,3642
Non-polymers5381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-3 kcal/mol
Surface area9430 Å2
MethodPISA
2
C: Protease
D: PVI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9023
Polymers24,3642
Non-polymers5381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-4 kcal/mol
Surface area9460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.733, 41.733, 193.552
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLEULEUAA1 - 2041 - 204
21SERSERLEULEUCC1 - 2041 - 204
12GLYGLYTYRTYRBB300 - 3101 - 11
22GLYGLYTYRTYRDD300 - 3101 - 11

NCS ensembles :
ID
1
2

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Components

#1: Protein Protease


Mass: 22993.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus D serotype 8 / Gene: L3 / Production host: Escherichia coli (E. coli) / References: UniProt: B9A5C1, adenain
#2: Protein/peptide PVI


Mass: 1370.691 Da / Num. of mol.: 2 / Fragment: UNP residues 223-233 / Source method: obtained synthetically / Source: (synth.) Human adenovirus D serotype 8 / References: UniProt: B9A5F5
#3: Chemical ChemComp-3VK / N-[(2S)-2-(3,5-dichlorophenyl)-2-(ethylamino)acetyl]-3-methyl-L-valyl-N-[3-(methylsulfonyl)propyl]glycinamide


Mass: 537.500 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H34Cl2N4O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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 Å3/Da / Density % sol: 38.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M Na citrate, 20% w/v PEG3350, 5 mg/ml protein, 2 mM inhibitor

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.52
11K, H, -L20.48
ReflectionResolution: 2.15→36.15 Å / Num. obs: 17707 / % possible obs: 86.3 % / Observed criterion σ(I): -3 / Redundancy: 3.66 % / Biso Wilson estimate: 27.206 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.062 / Χ2: 0.975 / Net I/σ(I): 15.86 / Num. measured all: 64802
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
2.15-2.210.8880.272.65227815539230.32859.4
2.21-2.270.9920.05713.36123114446440.07144.6
2.27-2.330.9250.2283.75245414729870.27767.1
2.33-2.40.9520.1564.492878136711500.18984.1
2.4-2.480.9790.1175.723151136211490.1484.4
2.48-2.570.9820.1057.153491130611880.12691
2.57-2.670.9820.1168.513500124510960.13788
2.67-2.780.9880.1058.813694126311740.12593
2.78-2.90.9920.08112.284199113611110.09497.8
2.9-3.040.9960.06716.084579109910940.07699.5
3.04-3.210.9950.0620.225184108110800.06899.9
3.21-3.40.9970.05822.4148519899800.06599.1
3.4-3.630.9940.062439249319120.06998
3.63-3.930.9930.05625.3930108738420.06796.4
3.93-4.30.9980.04330.1639418218180.04999.6
4.3-4.810.9980.04131.9134217397320.04699.1
4.81-5.550.9970.0429.4626576366350.04699.8
5.55-6.80.9980.03730.7427635515510.042100
6.8-9.620.9990.03137.6123074064060.035100
9.620.9990.02838.1912892352350.031100

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Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.8.0071refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→36.14 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.905 / SU B: 8.768 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2857 817 5 %RANDOM
Rwork0.2101 15394 --
obs0.2139 15394 79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.03 Å2 / Biso mean: 36.819 Å2 / Biso min: 14.45 Å2
Baniso -1Baniso -2Baniso -3
1-11.95 Å20 Å20 Å2
2--11.95 Å20 Å2
3----23.9 Å2
Refinement stepCycle: final / Resolution: 2.15→36.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3394 0 68 28 3490
Biso mean--42.98 27.62 -
Num. residues----430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193564
X-RAY DIFFRACTIONr_angle_refined_deg2.0511.9724826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1465428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5122165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.16415563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9651534
X-RAY DIFFRACTIONr_chiral_restr0.1290.2493
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212778
X-RAY DIFFRACTIONr_mcbond_it3.3623.6191718
X-RAY DIFFRACTIONr_mcangle_it4.7325.4212141
X-RAY DIFFRACTIONr_scbond_it3.7683.7721846
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A2580.3
12C2580.3
21B40.16
22D40.16
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 42 -
Rwork0.184 804 -
all-846 -
obs--54.55 %

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