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- PDB-5utn: Kaposi's Sarcoma Herpesvirus Protease in Complex with Allosteric ... -

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Basic information

Entry
Database: PDB / ID: 5utn
TitleKaposi's Sarcoma Herpesvirus Protease in Complex with Allosteric Inhibitor
ComponentsORF 17
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Serine Hydrolase / Viral Protein / Capsid Maturation / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


assemblin / viral release from host cell / host cell cytoplasm / serine-type endopeptidase activity / host cell nucleus / proteolysis / identical protein binding
Similarity search - Function
Serine Protease, Human Cytomegalovirus Protease; Chain A / Herpesvirus/Caudovirus protease domain / Peptidase S21 / Herpesvirus protease superfamily / Assemblin (Peptidase family S21) / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-8MA / Capsid scaffolding protein
Similarity search - Component
Biological speciesHuman herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsAcker, T.M. / Gable, J. / Bohn, M.-F. / Craik, C.S.
CitationJournal: To Be Published
Title: Kaposi's Sarcoma Herpesvirus Protease in Complex with Allosteric Inhibitor
Authors: Acker, T.M. / Craik, C.S. / Bohn, M.-F.
History
DepositionFeb 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORF 17
B: ORF 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8007
Polymers42,3862
Non-polymers1,4135
Water4,107228
1
A: ORF 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6412
Polymers21,1931
Non-polymers4481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ORF 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1595
Polymers21,1931
Non-polymers9664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.356, 95.801, 119.253
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-203-

CL

21B-204-

CL

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Components

#1: Protein ORF 17 / ORF17


Mass: 21193.111 Da / Num. of mol.: 2 / Fragment: residues 23-215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 / Gene: ORF17 / Production host: Escherichia coli (E. coli) / References: UniProt: O40922
#2: Chemical ChemComp-8MA / 4-{[6-(cyclohexylmethyl)pyridine-2-carbonyl]amino}-3-[(4-fluorophenyl)amino]benzoic acid


Mass: 447.501 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H26FN3O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1M Sodium acetate pH 7.8, 0.88M NaH2PO4/1.32M K2HPO4, 0.2M KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→59.63 Å / Num. obs: 72019 / % possible obs: 100 % / Redundancy: 14.3 % / Net I/σ(I): 24.64

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Processing

Software
NameVersionClassification
PHENIX1.10pre_2100refinement
PDB_EXTRACT3.22data extraction
SCALA3.3.21data scaling
PHENIXPhenix 1.8.4 Phaser 2.1phasing
MOSFLMdata reduction
RefinementResolution: 1.8→56.707 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.5 / Phase error: 25.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2287 3741 5.19 %
Rwork0.199 68278 -
obs0.2006 37695 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.35 Å2 / Biso mean: 36.5033 Å2 / Biso min: 13.12 Å2
Refinement stepCycle: final / Resolution: 1.8→56.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2867 0 176 228 3271
Biso mean--31.87 39.64 -
Num. residues----377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053079
X-RAY DIFFRACTIONf_angle_d0.8574230
X-RAY DIFFRACTIONf_chiral_restr0.05488
X-RAY DIFFRACTIONf_plane_restr0.006538
X-RAY DIFFRACTIONf_dihedral_angle_d13.9611798
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.82280.271410.24922472261399
1.8228-1.84680.3241420.24732507264999
1.8468-1.87210.30751670.239725302697100
1.8721-1.89880.30241280.23842516264499
1.8988-1.92720.29291280.240925092637100
1.9272-1.95730.26881330.2352587272099
1.9573-1.98940.2421170.226424922609100
1.9894-2.02370.2781270.222625372664100
2.0237-2.06050.23651460.219725582704100
2.0605-2.10010.24651270.222525312658100
2.1001-2.1430.22621280.210725232651100
2.143-2.18960.29131340.217525342668100
2.1896-2.24050.2941390.222125492688100
2.2405-2.29650.26511550.21524972652100
2.2965-2.35860.23541260.214525312657100
2.3586-2.4280.25391400.213425552695100
2.428-2.50640.24291250.217225482673100
2.5064-2.5960.25021420.222525312673100
2.596-2.69990.25921540.220225342688100
2.6999-2.82280.31421240.218425452669100
2.8228-2.97160.2481640.212124922656100
2.9716-3.15780.22251400.200825112651100
3.1578-3.40160.21111470.181325592706100
3.4016-3.74380.20761560.178225032659100
3.7438-4.28540.19181170.169625632680100
4.2854-5.39850.1591460.152925292675100
5.3985-56.7350.2071480.197325352683100

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