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- PDB-2wpo: HCMV protease inhibitor complex -

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Basic information

Entry
Database: PDB / ID: 2wpo
TitleHCMV protease inhibitor complex
ComponentsHUMAN CYTOMEGALOVIRUS PROTEASE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / VIRAL PROTEASE / HYDROLASE-HYDROLASE INHIBITOR complex / COAT PROTEIN / SERINE PROTEASE
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
BILC 821 / Chem-01E / Capsid scaffolding protein
Similarity search - Component
Biological speciesHuman herpesvirus 5
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTong, L. / Qian, C. / Massariol, M.-J. / Deziel, R. / Yoakim, C. / Lagace, L.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: Conserved mode of peptidomimetic inhibition and substrate recognition of human cytomegalovirus protease.
Authors: Tong, L. / Qian, C. / Massariol, M.J. / Deziel, R. / Yoakim, C. / Lagace, L.
#1: Journal: Nature / Year: 1996
Title: A New Serine-Protease Fold Revealed by the Crystal Structure of Human Cytomegalovirus Protease
Authors: Tong, L. / Qian, C. / Massariol, M.J. / Bonneau, P.R. / Cordingley, M.G. / Lagace, L.
History
DepositionAug 4, 1998Processing site: BNL
Revision 1.0Aug 4, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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 1.4Nov 3, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.6Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUMAN CYTOMEGALOVIRUS PROTEASE
B: HUMAN CYTOMEGALOVIRUS PROTEASE
C: HUMAN CYTOMEGALOVIRUS PROTEASE
D: HUMAN CYTOMEGALOVIRUS PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,5538
Polymers112,7154
Non-polymers2,8384
Water00
1
A: HUMAN CYTOMEGALOVIRUS PROTEASE
B: HUMAN CYTOMEGALOVIRUS PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7774
Polymers56,3572
Non-polymers1,4192
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-12 kcal/mol
Surface area20320 Å2
MethodPISA
2
C: HUMAN CYTOMEGALOVIRUS PROTEASE
D: HUMAN CYTOMEGALOVIRUS PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7774
Polymers56,3572
Non-polymers1,4192
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-13 kcal/mol
Surface area20240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.800, 53.400, 212.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
DetailsTHERE ARE FOUR MOLECULES IN THE ASYMMETRIC UNIT, FORMING TWO NON-CRYSTALLOGRAPHIC DIMERS.

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Components

#1: Protein
HUMAN CYTOMEGALOVIRUS PROTEASE


Mass: 28178.676 Da / Num. of mol.: 4 / Mutation: A143Q, T181M, L229M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 5 / Production host: Escherichia coli (E. coli)
References: UniProt: P16753, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical
ChemComp-01E / (2S)-2-(3,3-dimethylbutanoylamino)-N-[(2S)-1-[[(2S,3S)-3-hydroxy-4-[(4-iodophenyl)methylamino]-4-oxo-butan-2-yl]amino]- 1,4-dioxo-4-pyrrol-1-yl-butan-2-yl]-3,3-dimethyl-butanamide / BILC 821


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 709.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H44IN5O6 / References: BILC 821
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: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17 mg/mlprotein1drop
218 %PEG40001reservoir
30.1 MHEPES1reservoirpH7.5
40.2 M1reservoirNaCl
510 %glycerol1reservoir
650 mMspermine1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceWavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 33502 / % possible obs: 93 % / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.078
Reflection
*PLUS
Num. measured all: 275527

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Processing

Software
NameClassification
REPLACEmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
REPLACEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WPO

1wpo


Resolution: 2.7→6 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.332 -7.5 %RANDOM
Rwork0.226 ---
obs0.226 27152 92 %-
Refinement stepCycle: LAST / Resolution: 2.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7220 0 172 0 7392
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS

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