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- PDB-3em4: Crystal structure of atazanavir (ATV) in complex with I50L/A71V d... -

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Basic information

Entry
Database: PDB / ID: 3em4
TitleCrystal structure of atazanavir (ATV) in complex with I50L/A71V drug-resistant HIV-1 protease
ComponentsProtease
KeywordsHYDROLASE / drug resistance / hypersusceptibility / protease inhibitor / hiv / atazanavir / AIDS / Protease
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-DR7 / PHOSPHATE ION / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHIV-1 M:B_ARV2/SF2 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsPrabu-Jeyabalan, M. / King, N. / Royer, C. / Schiffer, C.
CitationJournal: To be Published
Title: Kinetic and Structural studies on atazanavir-specific I50L drug-resistant HIV-1 protease mutant
Authors: Prabu-Jeyabalan, M. / King, N. / Bandaranayake, R. / Nalivaika, E. / Schiffer, C.
History
DepositionSep 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Oct 20, 2021Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease
B: Protease
U: Protease
V: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,39413
Polymers43,3194
Non-polymers2,0759
Water2,810156
1
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7447
Polymers21,6602
Non-polymers1,0855
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-58 kcal/mol
Surface area8850 Å2
MethodPISA
2
U: Protease
V: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6496
Polymers21,6602
Non-polymers9904
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-56 kcal/mol
Surface area9000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.231, 59.540, 59.863
Angle α, β, γ (deg.)90.000, 82.220, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protease / / Retropepsin / PR


Mass: 10829.816 Da / Num. of mol.: 4 / Fragment: UNP residues 491-589 / Mutation: Q7K, I50L, A71V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_ARV2/SF2 (virus) / Strain: HXB2 / Gene: gag-pol, HIV-1 subtype B / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP106 / References: UniProt: P03369, HIV-1 retropepsin
#2: Chemical ChemComp-DR7 / (3S,8S,9S,12S)-3,12-BIS(1,1-DIMETHYLETHYL)-8-HYDROXY-4,11-DIOXO-9-(PHENYLMETHYL)-6-[[4-(2-PYRIDINYL)PHENYL]METHYL]-2,5, 6,10,13-PENTAAZATETRADECANEDIOIC ACID DIMETHYL ESTER / ATAZANAVIR / METHYL [(1S,4S,5S,10S)-4-BENZYL-1,10-DI-TERT-BUTYL-5-HYDROXY-2,9,12-TRIOXO-7-(4-PYRIDIN-2-YLBENZYL)-13-OXA-3,7,8,11-TETRAAZATET RADEC-1-YL]CARBAMATE / Atazanavir


Mass: 704.855 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C38H52N6O7 / Details: atazanavir is synthesized chemically / Comment: medication, antiretroviral*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.09 Å3/Da / Density % sol: 41.1 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 17, 2007 / Details: Yale Mirrors
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 56701 / Num. obs: 20006 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.069 / Χ2: 1.012 / Net I/σ(I): 14.007
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.180.49318671.035190.1
2.18-2.260.4219751.072195.3
2.26-2.370.34820071.05196.5
2.37-2.490.29119841.054196
2.49-2.650.21120051.118196.6
2.65-2.850.14920421.068197
2.85-3.140.09620121.052197.1
3.14-3.590.05720150.991196.8
3.59-4.520.0420480.867197.2
4.52-500.03520510.852195.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT3.006data extraction
AMoREphasing
RefinementStarting model: 1F7A

1f7a


Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0 / SU B: 10.946 / SU ML: 0.172 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.284 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1016 5.1 %RANDOM
Rwork0.179 ---
obs0.183 20000 95.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.01 Å2 / Biso mean: 38.666 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--2.13 Å20 Å20.25 Å2
2--1.04 Å20 Å2
3---1.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2937 0 137 156 3230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223127
X-RAY DIFFRACTIONr_bond_other_d0.0020.023024
X-RAY DIFFRACTIONr_angle_refined_deg1.4132.0284278
X-RAY DIFFRACTIONr_angle_other_deg0.71936986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2435392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.7124.8100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56715484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2461514
X-RAY DIFFRACTIONr_chiral_restr0.080.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023390
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02562
X-RAY DIFFRACTIONr_nbd_refined0.1890.2506
X-RAY DIFFRACTIONr_nbd_other0.2020.23024
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21416
X-RAY DIFFRACTIONr_nbtor_other0.0870.21917
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2116
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.2105
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.210
X-RAY DIFFRACTIONr_mcbond_it0.8881.52499
X-RAY DIFFRACTIONr_mcbond_other0.1641.5824
X-RAY DIFFRACTIONr_mcangle_it1.06823163
X-RAY DIFFRACTIONr_scbond_it1.58531317
X-RAY DIFFRACTIONr_scangle_it2.2744.51115
LS refinement shellResolution: 2.1→2.158 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 73 -
Rwork0.264 1284 -
all-1357 -
obs--88.63 %
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)
111.1777-7.47812.84676.5980.02243.0529-0.8283-1.29321.08190.53630.7213-0.4199-0.33220.35620.1070.03110.094-0.06510.1085-0.21750.05189.13515.55139.9229
214.0337-2.08054.62740.3096-0.72752.93870.19221.00231.8064-0.4442-0.1202-0.33750.2926-0.3036-0.072-0.0813-0.00010.047-0.02140.15950.25739.595916.113126.9049
310.89878.25-3.295219.7413-1.27591.1063-0.4071-2.6669-1.3490.25620.4051-0.13480.435-0.36140.0020.02140.1830.07380.22510.0824-0.06538.06012.928842.7619
47.8147-2.86032.71793.5220.50051.8486-0.3387-0.61440.1957-0.09930.2864-0.08140.38730.12090.0523-0.04640.03240.0019-0.0208-0.0129-0.034714.98575.671732.7736
513.0002-2.13821.26933.5317-3.48713.50370.0857-0.07980.054-0.24210.0316-0.448-0.12-0.0509-0.1172-0.0854-0.013-0.0023-0.02-0.0551-0.026829.2021-1.5228.3511
69.8956-2.39992.84181.1097-0.76631.3552-0.2088-0.07090.3627-0.00710.07980.01080.06470.25710.129-0.05530.02070.0083-0.0666-0.0266-0.09413.24156.643131.4834
75.23-0.4934-2.05244.3703-2.059110.374-0.12050.3033-0.14090.05760.10880.24870.1548-0.77540.0118-0.1374-0.0149-0.0098-0.0324-0.07250.0399-10.491.180924.8003
89.2087-5.46276.80474.4972-2.08428.06120.2679-0.0093-1.2218-0.4767-0.04440.51720.44160.1833-0.2235-0.0707-0.03210.0254-0.1753-0.03670.161717.0196-7.697527.8967
915.18681.38212.48087.61310.53431.87510.48642.3595-0.9736-0.1344-0.26550.35210.3840.5233-0.2209-0.05670.03710.00660.278-0.1625-0.10352.00580.596318.6909
107.87540.1576-3.17615.25899.31137.04180.1148-0.217-0.33290.1170.9142-0.6454-0.2252-0.193-1.029-0.07090.0504-0.01840.01740.0248-0.049328.116-2.488433.8679
1118.2734-3.65617.15775.2188-11.745931.5110.6068-0.02881.0244-0.0018-1.1623-0.13990.5956-0.21680.5555-0.1302-0.0286-0.1275-0.0405-0.0990.147325.990611.806435.8702
125.588-2.6613.571614.27870.96772.83-0.251-0.5680.25260.46480.2843-0.75090.2434-0.0436-0.0333-0.11070.07770.02050.1209-0.0621-0.097325.09645.319237.7453
133.8537-4.9916-3.48447.99088.168611.9099-0.0250.4592-0.12-0.1072-0.06760.8868-0.24620.07750.0926-0.1236-0.0419-0.04220.02430.0207-0.0343-9.54416.542622.797
1440.00950.783918.13643.70248.648626.87520.1189-0.4995-0.48040.16810.03370.5413-0.31420.2476-0.15250.0105-0.01090.0323-0.17960.0348-0.0163-8.131110.538736.7741
153.9225-2.9092-0.13736.93324.02727.701-0.0669-0.0010.2486-0.0777-0.20740.4216-0.1433-0.10550.2743-0.1017-0.02220.0047-0.0286-0.01730.002-7.38511.729330.8046
167.6788-2.8017-4.44097.17411.43538.06370.48840.28490.4042-0.6053-0.3643-0.1368-0.3905-0.1183-0.1241-0.07530.0294-0.0138-0.0477-0.02-0.108718.76383.152426.2897
1713.71216.9886.10459.40913.14995.35980.60150.1305-1.1441.0301-0.47780.30631.08640.2852-0.12370.02740.04660.006-0.0656-0.08510.0701-0.4998-0.079829.6807
1816.5054-4.07466.83325.9622-0.76394.0066-0.757-1.75760.69010.53730.9594-0.7156-0.1303-0.0481-0.2024-0.03150.1197-0.05960.1998-0.1075-0.043117.73147.024639.9924
1911.4761-7.0064-1.24635.88381.42910.41340.04190.12440.50280.10660.16620.0139-0.2028-0.0422-0.2081-0.07240.0093-0.0061-0.0674-0.00520.01750.455713.958731.6352
208.1803-4.70345.96464.3125-2.23755.23240.02020.3031-0.1402-0.1963-0.1502-0.45370.02110.03930.13-0.05470.03810.02210.06350.0123-0.02639.36552.367127.761
212.8506-1.5695-2.49552.8416-0.74354.4524-0.2624-0.5003-0.38820.32770.06960.00640.2109-0.05730.1927-0.04640.00660.0146-0.00430.0926-0.064220.256-7.662812.2657
228.7858-1.2732-0.99225.86140.335613.5879-0.2472-1.06640.8668-0.0130.5354-0.2707-0.21290.047-0.2882-0.08070.0512-0.0559-0.0645-0.0922-0.085321.00645.691812.0215
238.16326.9216-3.18466.0915-1.31989.80270.38860.5109-0.5888-0.1701-0.03840.0557-0.0615-0.2931-0.3503-0.0287-0.00680.0261-0.1302-0.0642-0.048919.5951-11.3959-0.3808
243.56950.3610.16192.52660.01392.9967-0.2438-0.137-0.0323-0.01650.00110.2142-0.08640.13320.2428-0.010.0392-0.0037-0.0591-0.0162-0.106426.2409-1.28131.9029
252.5781.77510.86841.41311.2119.765-0.03720.09590.04380.23110.1670.0468-0.0730.6804-0.1299-0.1182-0.0255-0.0112-0.02760.0635-0.006840.0132.023-5.961
268.30570.59820.09670.8311-0.85340.9404-0.0344-0.22920.06920.14230.1008-0.0906-0.1531-0.0764-0.0664-0.04880.02430.0103-0.0661-0.0261-0.065714.5080.09232.6955
2710.792-1.01490.66335.92410.70543.48760.1002-0.09850.1689-0.1217-0.17290.26920.2808-0.53320.0727-0.1087-0.0090.0267-0.01260.0275-0.08750.36936.6478-2.5154
2815.4241-1.5738-6.82165.29141.15254.13850.22120.3180.2382-0.455-0.15410.0673-0.1637-0.0379-0.0671-0.04910.0105-0.0222-0.0310.0033-0.157928.04372.0024-11.8352
2914.6147-8.7744-2.767911.59950.88950.6184-0.02870.48710.087-0.17240.07530.0863-0.0232-0.2341-0.0465-0.0886-0.0119-0.0297-0.12140.0095-0.038612.67712.6608-4.3381
301.9629-2.72664.2895.4871-5.36879.5753-0.04970.249-0.16260.0568-0.06810.0221-0.23510.3550.1178-0.0722-0.00320.02740.00410.0136-0.001839.2192-3.2631-6.2375
313.6357-2.6931-4.225614.3165-3.4988.4767-0.0452-0.6720.66950.26160.6803-0.28450.47210.4197-0.6351-0.06320.0082-0.05780.0109-0.0166-0.036937.498-3.91928.3634
321.6502-1.1513.57135.3759-3.78038.0923-0.0144-0.00680.1158-0.0760.024-0.28460.157-0.427-0.0096-0.0658-0.00240.0114-0.0567-0.01050.013936.3428-6.30831.9927
337.16615.2387-4.95769.6703-11.299113.5150.0788-0.35070.7375-0.22340.24050.19010.3512-0.2988-0.3193-0.0790.0789-0.0167-0.047-0.042-0.01251.58488.4341.9568
3412.3053-19.55337.156836.3955-13.28644.8505-0.12630.7615-0.10890.6882-0.3672-0.0851-0.04160.04170.4935-0.01550.02280.00450.0188-0.0003-0.08853.2023-5.22896.9771
350.37891.7624-1.937113.4444-7.982810.1062-0.145-0.27290.14140.4013-0.1863-0.4439-0.1657-0.04980.3313-0.10940.0299-0.00390.05980.0149-0.04474.37931.57397.4445
363.5069-0.3384-4.31528.2924-3.30326.98480.0782-0.01350.21370.31180.3957-0.0411-0.3821-0.0824-0.4739-0.07790.0029-0.0399-0.0290.00660.020129.93854.9235-1.2935
3710.175-3.84531.85192.544-2.46653.1983-0.2036-0.1697-0.48510.00650.0464-0.38170.18440.0250.1572-0.08290.0030.0083-0.11350.0134-0.020329.1025-8.40793.7396
385.81010.97580.95641.06781.79643.1177-0.2032-0.6776-0.18670.01220.04060.21350.0377-0.21620.1626-0.07310.03390.04950.045-0.0012-0.109711.61130.509810.016
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION1A94 - 99
3X-RAY DIFFRACTION1B1 - 5
4X-RAY DIFFRACTION1B94 - 99
5X-RAY DIFFRACTION2A6 - 10
6X-RAY DIFFRACTION3B6 - 10
7X-RAY DIFFRACTION4A22 - 32
8X-RAY DIFFRACTION5A33 - 43
9X-RAY DIFFRACTION6B22 - 32
10X-RAY DIFFRACTION7B33 - 43
11X-RAY DIFFRACTION8A44 - 49
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