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- PDB-1nkk: COMPLEX STRUCTURE OF HCMV PROTEASE AND A PEPTIDOMIMETIC INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 1nkk
TitleCOMPLEX STRUCTURE OF HCMV PROTEASE AND A PEPTIDOMIMETIC INHIBITOR
Components
  • Capsid protein P40
  • Peptidomimetic inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PROTEASE / PEPTIDOMIMETIC INHIBITOR / INDUCED-FIT / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


assemblin / nuclear capsid assembly / 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-acetyl-L-valyl-3,3-dimethyl-L-alpha-aspartyl-N~4~,N~4~-dimethyl-N~1~-[(1R)-3,3,3-trifluoro-1-methyl-2-oxopropyl]-L-as partamide / Capsid scaffolding protein
Similarity search - Component
Biological speciesHuman herpesvirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / COMO / Resolution: 2.6 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 / 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein P40
B: Capsid protein P40
C: Capsid protein P40
D: Capsid protein P40
E: Peptidomimetic inhibitor
F: Peptidomimetic inhibitor
G: Peptidomimetic inhibitor
H: Peptidomimetic inhibitor


Theoretical massNumber of molelcules
Total (without water)114,8418
Polymers114,8418
Non-polymers00
Water4,486249
1
A: Capsid protein P40
B: Capsid protein P40
E: Peptidomimetic inhibitor
F: Peptidomimetic inhibitor


Theoretical massNumber of molelcules
Total (without water)57,4204
Polymers57,4204
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-14 kcal/mol
Surface area19390 Å2
MethodPISA
2
C: Capsid protein P40
D: Capsid protein P40
G: Peptidomimetic inhibitor
H: Peptidomimetic inhibitor


Theoretical massNumber of molelcules
Total (without water)57,4204
Polymers57,4204
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-18 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.170, 215.250, 52.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Capsid protein P40 / Protease / Capsid assembly protein


Mass: 28158.627 Da / Num. of mol.: 4 / Fragment: Assemblin / Mutation: A143Q, E31R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 5 / Genus: Cytomegalovirus / Gene: UL80 OR APNG / Production host: Escherichia coli (E. coli) / References: UniProt: P16753, assemblin
#2: Protein/peptide
Peptidomimetic inhibitor


Type: Peptide-like / Class: Inhibitor / Mass: 551.557 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: Residue peptide of the Peptidomimetic Inhibitor was chemically synthesized.
References: N-acetyl-L-valyl-3,3-dimethyl-L-alpha-aspartyl-N~4~,N~4~-dimethyl-N~1~-[(1R)-3,3,3-trifluoro-1-methyl-2-oxopropyl]-L-as partamide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.58 Å3/Da / Density % sol: 52.37 %
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: APS / Beamline: 19-BM / Wavelength: 0.97799 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 9, 2002
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97799 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 38225 / Num. obs: 38225 / % possible obs: 91 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 18 Å2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 82.1
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / % possible obs: 91 % / Num. measured all: 103436 / Rmerge(I) obs: 0.099

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: COMO / Resolution: 2.6→19.98 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 797979.9 / Data cutoff high rms absF: 797979.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 2179 7 %RANDOM
Rwork0.233 ---
obs0.233 30941 82.6 %-
all-30941 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.952 Å2 / ksol: 0.346262 e/Å3
Displacement parametersBiso mean: 17.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2---1.86 Å20 Å2
3---1.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7182 0 0 249 7431
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it2.192
X-RAY DIFFRACTIONc_scbond_it1.632
X-RAY DIFFRACTIONc_scangle_it2.572.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.366 299 6.9 %
Rwork0.314 4058 -
obs--70.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM.HCMVTOP.HCMV
X-RAY DIFFRACTION3WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95

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