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- PDB-4j5j: Crystal Structure of Multidrug Resistant HIV-1 Protease Clinical ... -

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Basic information

Entry
Database: PDB / ID: 4j5j
TitleCrystal Structure of Multidrug Resistant HIV-1 Protease Clinical Isolate PR20 in Complex with Amprenavir
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / multidrug resistant HIV-1 protease clinical isolate PR20 / clinical inhibitor Amprenavir / potent antiviral inhibitor GRL-0519A / potent antiviral inhibitor GRL-02031 / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


RNA stem-loop binding / host cell / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...RNA stem-loop binding / host cell / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain ...Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-478 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsShen, C.H. / Weber, I.T.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Extreme Multidrug Resistant HIV-1 Protease with 20 Mutations Is Resistant to Novel Protease Inhibitors with P1'-Pyrrolidinone or P2-Tris-tetrahydrofuran.
Authors: Agniswamy, J. / Shen, C.H. / Wang, Y.F. / Ghosh, A.K. / Rao, K.V. / Xu, C.X. / Sayer, J.M. / Louis, J.M. / Weber, I.T.
History
DepositionFeb 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6517
Polymers21,5332
Non-polymers1,1185
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-43 kcal/mol
Surface area10550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.717, 65.798, 93.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protease /


Mass: 10766.542 Da / Num. of mol.: 2 / Fragment: UNP residues 501-599
Mutation: Q7K,L10F,I13V,I15V,D30N,V32I,L33F,E35D,M36I,S37N,I47V,I54L,Q58E,I62V,L63P,A71V,I84V,N88D,L89T,L90M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03367, HIV-1 retropepsin
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-478 / {3-[(4-AMINO-BENZENESULFONYL)-ISOBUTYL-AMINO]-1-BENZYL-2-HYDROXY-PROPYL}-CARBAMIC ACID TETRAHYDRO-FURAN-3-YL ESTER / Amprenavir / Amprenavir


Mass: 505.627 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H35N3O6S / Comment: protease inhibitor, medication*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.05 Å3/Da / Density % sol: 40.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 1.67 M sodium chloride, 67 mM citrate/phosphate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.84999 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 13, 2009 / Details: mirrors
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84999 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 17214 / Num. obs: 16791 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 19.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.8-1.863.10.4682.1180
1.86-1.94195.2
1.94-2.03199.8
2.03-2.13199.9
2.13-2.271100
2.27-2.441100

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UCB

3ucb


Resolution: 1.8→9.91 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.855 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24279 828 5 %RANDOM
Rwork0.18743 ---
obs0.19015 15764 97.65 %-
all-17214 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.471 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2---0.05 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.8→9.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 73 95 1686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221652
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1082.022251
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.025204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88924.23759
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44615277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.208159
X-RAY DIFFRACTIONr_chiral_restr0.1560.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211199
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.2703
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21124
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0830.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4271.5990
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.39421620
X-RAY DIFFRACTIONr_scbond_it3.1993662
X-RAY DIFFRACTIONr_scangle_it5.184.5627
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 53 -
Rwork0.255 868 -
obs--77.98 %
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)
10.6015-0.36571.21371.77171.34855.5204-0.0132-0.0204-0.06460.0925-0.0410.01550.2177-0.07760.05420.0381-0.02550.05220.04590.01870.100613.8609-12.1299-8.8418
20.63450.1521-0.0813-0.02010.10233.9023-0.0551-0.0629-0.1108-0.0092-0.0234-0.02170.2160.07170.07850.1757-0.00730.02310.05910.00040.104212.931-15.3042-8.3015
31.0975-0.17350.35430.48320.06364.30080.0956-0.02390.1909-0.04340.0927-0.0288-0.27-0.0877-0.18830.0735-0.01450.03310.0262-0.00920.114513.26916.3077-10.6516
4-0.0338-0.0672-0.59620.00980.49981.8671-0.0192-0.0203-0.00870.05180.0544-0.02540.24350.0589-0.03510.18020.01750.00590.06710.01040.143412.5525-12.0001-9.0136
53.7120.51662.42330.0758-0.02184.97050.1257-0.12030.09780.0053-0.07050.02650.2171-0.0643-0.05510.095-0.0013-0.02240.0319-0.02710.090912.7046-1.1132-9.8833
60.46410.03580.2490.8595-0.22110.62650.0108-0.01170.0344-0.0115-0.021-0.0062-0.07450.00060.01020.09420.00520.00010.0941-0.01630.10913.31935.9928-10.295
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 44
2X-RAY DIFFRACTION1B135 - 144
3X-RAY DIFFRACTION2A45 - 57
4X-RAY DIFFRACTION2B145 - 157
5X-RAY DIFFRACTION3A64 - 72
6X-RAY DIFFRACTION3B164 - 172
7X-RAY DIFFRACTION4A78 - 82
8X-RAY DIFFRACTION4B178 - 182
9X-RAY DIFFRACTION5A13 - 20
10X-RAY DIFFRACTION5B113 - 120
11X-RAY DIFFRACTION6A1 - 8
12X-RAY DIFFRACTION6B101 - 108

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