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- PDB-3u7s: HIV PR drug resistant patient's variant in complex with darunavir -

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Basic information

Entry
Database: PDB / ID: 3u7s
TitleHIV PR drug resistant patient's variant in complex with darunavir
ComponentsPol polyprotein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / darunvir / resistance / mutation score / HIV protease / TMC-114 / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / 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 / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type superfamily / 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-017 / BETA-MERCAPTOETHANOL / Gag-Pol polyprotein / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.05 Å
AuthorsSaskova, K.G. / Rezacova, P. / Konvalinka, J. / Brynda, J. / Kozisek, M.
CitationJournal: J.Virol. / Year: 2009
Title: Molecular characterization of clinical isolates of human immunodeficiency virus resistant to the protease inhibitor darunavir.
Authors: Saskova, K.G. / Kozisek, M. / Rezacova, P. / Brynda, J. / Yashina, T. / Kagan, R.M. / Konvalinka, J.
History
DepositionOct 14, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionJan 18, 2012ID: 3GGT
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Advisory / Database references / Category: pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.2Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

Downloads & links

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Assembly

Deposited unit
A: Pol polyprotein
B: Pol polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9316
Polymers21,6792
Non-polymers1,2524
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-42 kcal/mol
Surface area9250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.540, 62.540, 82.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Pol polyprotein / HIV protease


Mass: 10839.683 Da / Num. of mol.: 2 / Fragment: unp residues 9-107
Mutation: T12V, I13V, I15V, K20M, V32I, L33F, K43T, I54L, K55N, I62V, L63P, A71V, I72V, G73S, V77I, V82L, I84V, L89V, L90M
Source method: isolated from a genetically manipulated source
Details: refolding from inclusion bodies / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL
References: UniProt: Q993Q5, UniProt: P35963*PLUS, HIV-1 retropepsin
#2: Chemical ChemComp-017 / (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE / Darunavir / TMC114 / UIC-94017


Mass: 547.664 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H37N3O7S / Comment: medication, antiretroviral*YM
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.84 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: protein at 5mg/ml, inhibitor:protein = 5:1, reservoir: 0.6M NaCl, 0.1M MES, drops: 2+1ul, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 12, 2008
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.05→45.3 Å / Num. all: 11987 / Num. obs: 11575 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.067
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.2 / % possible all: 98.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.05→45.3 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.882 / SU B: 10.913 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26772 553 4.8 %RANDOM
Rwork0.19022 ---
obs0.19391 10994 99.92 %-
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: 27.841 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.05→45.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 82 173 1773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221707
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7872.0272338
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.7565215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.78924.92163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44315275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.438159
X-RAY DIFFRACTIONr_chiral_restr0.1150.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021267
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.2850
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21142
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2159
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9421.51062
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.18721693
X-RAY DIFFRACTIONr_scbond_it1.8423728
X-RAY DIFFRACTIONr_scangle_it2.5874.5642
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 37 -
Rwork0.22 813 -
obs--99.65 %
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)
12.24290.5545-1.82820.7488-1.28228.00290.2068-0.00520.25680.12740.06440.2402-0.6528-0.4232-0.2712-0.01960.01630.0249-0.03560.0148-0.0564-19.0127.37925.855
26.04311.35930.31591.34931.07582.61670.04920.0326-0.0692-0.0971-0.10330.15390.033-0.08680.054-0.07460.0001-0.0102-0.0540.0059-0.1112-20.48516.87518.294
35.3988-1.99171.77983.7893-0.31046.2350.31860.7302-0.816-0.2771-0.01850.13920.75110.135-0.30010.047-0.009-0.0380.0842-0.16670.0763-11.7949.80113.176
41.44510.9178-1.36320.9116-1.4248.21750.07390.09310.35750.0738-0.05130.0543-0.6645-0.3648-0.0226-0.01730.02960.0096-0.02840.0132-0.0327-14.22630.18628.386
54.74642.9870.31983.6294-0.27892.1524-0.0685-0.04150.10790.12310.0144-0.0787-0.08520.08520.0542-0.0545-0.0125-0.0115-0.0847-0.0188-0.1252-4.34226.16435.973
61.51022.16373.91463.41595.488210.1935-0.08030.3068-0.1777-0.51541.0062-0.6286-0.57961.6594-0.92590.00320.01090.02630.00960.04660.0609-2.23915.14540.757
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 9
2X-RAY DIFFRACTION1A86 - 99
3X-RAY DIFFRACTION2A10 - 32
4X-RAY DIFFRACTION2A63 - 85
5X-RAY DIFFRACTION3A33 - 62
6X-RAY DIFFRACTION4B1 - 9
7X-RAY DIFFRACTION4B86 - 99
8X-RAY DIFFRACTION5B10 - 32
9X-RAY DIFFRACTION5B63 - 85
10X-RAY DIFFRACTION6B33 - 62

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