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- PDB-1nkm: Complex structure of HCMV Protease and a peptidomimetic inhibitor -

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Basic information

Entry
Database: PDB / ID: 1nkm
TitleComplex structure of HCMV Protease and a peptidomimetic inhibitor
ComponentsAssemblin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Protease / Peptidomimetic Inhibitor / Induced-fit / 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
N-(6-aminohexanoyl)-3-methyl-L-valyl-3-methyl-L-valyl-N~4~,N~4~-dimethyl-N~1~-[(1R)-1-methyl-2,3-dioxo-3-{[(1S)-1- phenylpropyl]amino}propyl]-L-aspartamide / Chem-0FP / Capsid scaffolding protein
Similarity search - Component
Biological speciesHuman herpesvirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / COMO / Resolution: 2.7 Å
AuthorsKhayat, R. / Batra, R. / Qian, C. / Halmos, T. / Bailey, M. / Tong, L.
CitationJournal: Biochemistry / Year: 2003
Title: Structural and Biochemical Studies of Inhibitor Binding to Human Cytomegalovirus Protease
Authors: Khayat, R. / Batra, R. / Qian, C. / Halmos, T. / Bailey, M. / Tong, L.
History
DepositionJan 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Mar 13, 2024Group: Data collection / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity / pdbx_entity_src_syn
Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Assemblin
B: Assemblin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9793
Polymers56,2612
Non-polymers7181
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-17 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.880, 73.880, 216.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Assemblin / / Protease / Capsid assembly protein


Mass: 28130.547 Da / Num. of mol.: 2 / Mutation: A143Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 5 / Gene: UL80, APNG / Production host: Escherichia coli (E. coli) / References: UniProt: P16753, assemblin
#2: Chemical ChemComp-0FP / N-(6-aminohexanoyl)-3-methyl-L-valyl-3-methyl-L-valyl-N~1~-[(2S,3S)-3-hydroxy-4-oxo-4-{[(1R)-1-phenylpropyl]amino}butan-2-yl]-N~4~,N~4~-dimethyl-L-aspartamide / BILC 408


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 717.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H63N7O7
Details: Residue peptide of the Peptidomimetic Inhibitor was chemically synthesized.
References: N-(6-aminohexanoyl)-3-methyl-L-valyl-3-methyl-L-valyl-N~4~,N~4~-dimethyl-N~1~-[(1R)-1-methyl-2,3-dioxo-3-{[(1S)-1- phenylpropyl]amino}propyl]-L-aspartamide
Nonpolymer detailsTHE INHIBITOR 0FP IS COVALENTLY CONNECTED AT CARBON C4 TO THE ACTIVE SITE SERINE A 132 VIA HEMIKETAL LINKAGE

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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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, HEPES, EDTA, Sodium Chloride, Sodium Sulfate, DTT, Spermine_HCl, Glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 21 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17 mg/mlprotein1drop
220 mMHEPES1droppH7.0
380 mM1dropNa2SO4
440 mM1dropNaCl
52 mMdithiothreitol1drop
62 mMEDTA1drop
72 mMDMF1drop
816-18 %PEG40001reservoir
90.1 MHEPES1reservoirpH7.0
1010-12 %glycerol1reservoir
110.3 M1reservoirNaCl
125 mMspermine-HCl1reservoir
132 mMdithiothreitol1reservoir
142 mMEDTA1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 20, 2000
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 16733 / Num. obs: 16733 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 4.6 Å2
Reflection shellResolution: 2.7→2.8 Å / % possible all: 92.2
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. measured all: 66771 / Rmerge(I) obs: 0.063

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: COMO / Resolution: 2.7→19.71 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 0 / Data cutoff high rms absF: 2631533.36 / Data cutoff low absF: 2631533.36 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.298 952 6.8 %RANDOM
Rwork0.236 ---
obs0.236 13923 80.7 %-
all-13926 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.1713 Å2 / ksol: 0.299306 e/Å3
Displacement parametersBiso mean: 62 Å2
Baniso -1Baniso -2Baniso -3
1-14.93 Å20 Å20 Å2
2--22.98 Å20 Å2
3----37.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3452 0 51 0 3503
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.99
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.404 115 7.8 %
Rwork0.361 1362 -
obs--52.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM.HCMVTOP.HCMV
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.99

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