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- PDB-2pbk: Crystal structure of KSHV protease in complex with hexapeptide ph... -

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Basic information

Entry
Database: PDB / ID: 2pbk
TitleCrystal structure of KSHV protease in complex with hexapeptide phosphonate inhibitor
Components
  • KSHV protease
  • hexapeptide phosphonate inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / KSHV / KSHV PROTEASE / HERPESVIRUS PROTEASE / VIRAL PROTEASE / VIRAL PROTEIN / 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
1-acetyl-L-prolyl-L-valyl-L-tyrosyl-3-methyl-L-valyl-N~1~-[(1R)-1-phosphonoethyl]-L-glutamamide / ACETATE ION / Capsid scaffolding protein
Similarity search - Component
Biological speciesHuman herpesvirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsLazic, A. / Goetz, D.H.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Substrate modulation of enzyme activity in the herpesvirus protease family.
Authors: Lazic, A. / Goetz, D.H. / Nomura, A.M. / Marnett, A.B. / Craik, C.S.
History
DepositionMar 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Oct 20, 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_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_comp_id / _struct_conn.ptnr2_label_seq_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 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KSHV protease
B: KSHV protease
C: hexapeptide phosphonate inhibitor
D: hexapeptide phosphonate inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7367
Polymers51,5594
Non-polymers1773
Water9,548530
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-48 kcal/mol
Surface area19750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.883, 108.941, 54.051
Angle α, β, γ (deg.)90.00, 103.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein KSHV protease


Mass: 25027.662 Da / Num. of mol.: 2 / Mutation: S204G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus / Genus: Rhadinovirus / Strain: 8 / Gene: AF010430 / Plasmid: pet21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: O36607
#2: Protein/peptide hexapeptide phosphonate inhibitor


Type: Peptide-like / Class: Inhibitor / Mass: 751.808 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: solid phase FMOC
References: 1-acetyl-L-prolyl-L-valyl-L-tyrosyl-3-methyl-L-valyl-N~1~-[(1R)-1-phosphonoethyl]-L-glutamamide
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE ELECTRON DENSITY SURROUNDING THE PHOSPHONATE GROUP SHOWS THAT THE INHIBITOR IN THE CRYSTAL ...THE ELECTRON DENSITY SURROUNDING THE PHOSPHONATE GROUP SHOWS THAT THE INHIBITOR IN THE CRYSTAL EXISTS IN AN "AGED" FORM, WHERE THE PHENOXY GROUPS ATTACHED TO O1A AND O1B ARE RELEASED. IN ADDITION TO THE COVALENT LINK TO THE CATALYTIC SER 114, THE PHOSPHONATE IS STABILIZED BY A H BOND TO NE2 OF HIS 46

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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: 2.56 Å3/Da / Density % sol: 51.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.8M NaFormate, 0.1M NaAcetate, 5% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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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 210 / Detector: CCD / Date: Jun 24, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→20 Å / Num. all: 50932 / Num. obs: 47867 / % possible obs: 93.92 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.2
Reflection shellHighest resolution: 1.73 Å / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 4.8 / % possible all: 61.75

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1FL1

1fl1


Resolution: 1.73→19.57 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.02 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20394 2568 5.1 %RANDOM
Rwork0.16122 ---
obs0.16344 47865 93.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.575 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20.03 Å2
2--0.04 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.73→19.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3613 0 12 530 4155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223709
X-RAY DIFFRACTIONr_bond_other_d0.0010.023465
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.9865069
X-RAY DIFFRACTIONr_angle_other_deg0.81638025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8835470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.81923.05141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12815574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3321523
X-RAY DIFFRACTIONr_chiral_restr0.1490.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024063
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02718
X-RAY DIFFRACTIONr_nbd_refined0.2350.2817
X-RAY DIFFRACTIONr_nbd_other0.1830.23631
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21804
X-RAY DIFFRACTIONr_nbtor_other0.0840.22232
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2394
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0520.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.237
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0851.52422
X-RAY DIFFRACTIONr_mcbond_other0.2731.5933
X-RAY DIFFRACTIONr_mcangle_it1.63923834
X-RAY DIFFRACTIONr_scbond_it2.36231448
X-RAY DIFFRACTIONr_scangle_it3.5354.51230
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 136 -
Rwork0.227 2311 -
obs--61.78 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.15940.4254-0.04321.6779-0.8421.70680.0143-0.0320.014-0.0138-0.00830.0072-0.24530.0508-0.006-0.1043-0.00580.0076-0.129-0.0173-0.1214-2.25317.81223.423
21.6182-0.1753-0.0941.4778-0.08251.35010.0169-0.0562-0.0410.05380.03740.01360.1014-0.0802-0.0543-0.1512-0.0003-0.0218-0.1332-0.0025-0.1223-23.212-5.10943.378
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 230
2X-RAY DIFFRACTION1D1 - 6
3X-RAY DIFFRACTION2B3 - 230
4X-RAY DIFFRACTION2C1 - 6

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