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- PDB-3ekw: Crystal structure of the inhibitor Atazanavir (ATV) in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3ekw
TitleCrystal structure of the inhibitor Atazanavir (ATV) in complex with a multi-drug resistance HIV-1 protease variant (L10I/G48V/I54V/V64I/V82A) Refer: FLAP+ in citation.
ComponentsProtease
KeywordsHYDROLASE / HIV-1 / protease / multi-drug resistance / Atazanavir / AIDS
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 / telomerase activity / viral penetration into host nucleus / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / viral translational frameshifting / 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. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / Retroviral matrix protein / Cathepsin D, subunit A; domain 1 / Acid Proteases / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / 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. / Aspartic peptidase domain superfamily / Ribonuclease H 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsPrabu-Jeyabalan, M. / King, N.M. / Bandaranayake, R.M.
CitationJournal: Acs Chem.Biol. / Year: 2012
Title: Extreme Entropy-Enthalpy Compensation in a Drug-Resistant Variant of HIV-1 Protease.
Authors: King, N.M. / Prabu-Jeyabalan, M. / Bandaranayake, R.M. / Nalam, M.N. / Nalivaika, E.A. / Ozen, A. / Yilmaz, N.K. / Schiffer, C.A.
History
DepositionSep 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 25, 2012Group: Data collection / Database references
Revision 1.3Oct 17, 2012Group: Database references
Revision 1.4Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / 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 1.6Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6216
Polymers21,6322
Non-polymers9904
Water2,558142
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-47 kcal/mol
Surface area9000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.245, 58.483, 61.326
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protease / Retropepsin / PR


Mass: 10815.788 Da / Num. of mol.: 2 / Fragment: UNP residues 491-589 / Mutation: Q7K,L10I,G48V,I54V,V64I,V82A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_ARV2/SF2 (virus) / Gene: gag-pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP106 / References: UniProt: P03369, HIV-1 retropepsin
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: 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


Mass: 704.855 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H52N6O7 / Comment: medication, antiretroviral*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.12 Å3/Da / Density % sol: 42.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 16, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→42.33 Å / Num. all: 24185 / Num. obs: 24185 / % possible obs: 96.6 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 17.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
AMoREphasing
REFMAC5.2.0005refinement
PDB_EXTRACT3.006data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→42.33 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.414 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1236 5.1 %RANDOM
Rwork0.187 ---
obs0.189 24139 96.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.51 Å2 / Biso mean: 23.955 Å2 / Biso min: 13.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2---0.44 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.6→42.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1484 0 66 142 1692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221670
X-RAY DIFFRACTIONr_bond_other_d0.0010.021600
X-RAY DIFFRACTIONr_angle_refined_deg1.3922.0122297
X-RAY DIFFRACTIONr_angle_other_deg0.78233717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1065216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.8252554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49615270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.044157
X-RAY DIFFRACTIONr_chiral_restr0.0830.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021857
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02306
X-RAY DIFFRACTIONr_nbd_refined0.1840.3246
X-RAY DIFFRACTIONr_nbd_other0.170.31651
X-RAY DIFFRACTIONr_nbtor_refined0.1690.5817
X-RAY DIFFRACTIONr_nbtor_other0.0830.51063
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.5208
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1340.346
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.250.525
X-RAY DIFFRACTIONr_symmetry_hbond_other0.1120.51
X-RAY DIFFRACTIONr_mcbond_it0.7861.51349
X-RAY DIFFRACTIONr_mcbond_other0.1711.5430
X-RAY DIFFRACTIONr_mcangle_it0.89121705
X-RAY DIFFRACTIONr_scbond_it1.6093718
X-RAY DIFFRACTIONr_scangle_it2.3294.5592
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 94 -
Rwork0.335 1584 -
all-1678 -
obs--93.07 %
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)
13.27510.55610.18856.9734-1.26791.0318-0.0980.3919-0.0041-0.65040.09110.16360.0104-0.04810.0069-0.0397-0.0232-0.0385-0.007-0.0228-0.089920.5073.3851.717
22.31370.77730.34712.22850.62092.6614-0.08880.07020.3685-0.14160.04860.2492-0.162-0.14320.0402-0.1129-0.0069-0.0383-0.08180.01490.005919.94211.5677.328
314.99671.68574.52555.5111.88664.7573-0.06710.146-0.36330.03970.1139-0.46250.18650.1022-0.0468-0.13840.00240.0189-0.11070.0076-0.052338.97-2.1547.485
44.0475-0.9211-0.13543.24250.57751.8145-0.04830.05950.06590.0819-0.01360.12570.114-0.03520.0619-0.115-0.00870.002-0.0767-0.0027-0.059626.571.87512.854
511.9536-0.69211.78715.41191.4499.981-0.2144-0.37170.14070.04570.1125-0.672-0.30650.97540.1019-0.0845-0.025-0.01940.04650.05180.050840.067-1.8120.835
645.968711.0254-6.49384.12830.79114.63480.375-0.58410.96530.2445-0.25010.4125-0.0194-0.2132-0.1249-0.11790.007-0.003-0.04220.05250.13162.2657.90114.518
77.0741-0.5144-2.16394.2057-0.42050.9750.0650.11510.07050.0170.00310.2597-0.0291-0.0341-0.068-0.0973-0.0017-0.0274-0.0491-0.00350.018214.2731.13512.136
813.561.82710.72095.80330.42433.26420.0312-0.2098-0.0570.06380.0590.4605-0.1081-0.1536-0.0901-0.08330.01490.04440.01660.0510.02221.066-5.19318.276
922.5272.51923.76742.4901-0.49541.0106-0.0199-1.0020.04960.2164-0.05410.2946-0.0244-0.07750.0741-0.013-0.0290.00260.0587-0.0073-0.028726.333-0.95627.017
108.59115.4441.25438.35831.49151.55630.0042-0.22310.1150.4108-0.10830.3549-0.04820.0240.1041-0.05190.00150.0296-0.04540.00230.021314.711-10.10620.305
117.30155.6851-5.10410.9245-6.38558.71780.2454-0.4524-0.19330.3911-0.3633-0.22240.03610.24050.1179-0.165-0.0267-0.0456-0.06110.0045-0.081638.944.84921.098
1212.11240.0110.16787.83543.541226.6444-0.02190.6728-0.4953-0.47160.1981-0.2630.02970.515-0.1762-0.14190.00310.0282-0.1389-0.0077-0.072737.1564.8345.981
134.27931.50090.29892.02280.17173.58120.01430.03390.0834-0.1044-0.13680.00150.00710.32740.1225-0.14010.0156-0.0146-0.1202-0.0037-0.079836.3937.44811.934
1411.1272-5.36523.9148.9609-7.899710.5850.24060.3981-0.4877-0.16080.20480.4969-0.16370.2017-0.4453-0.1306-0.0366-0.0046-0.0841-0.03110.18691.899-7.22512.987
1524.442515.3-11.040428.2995-5.79410.3920.27530.43520.5987-0.33390.11430.6519-0.4311-0.1664-0.3896-0.09910.0007-0.011-0.02520.08610.03893.2346.8187.255
163.34580.66180.63692.9449-1.28590.82960.11080.4994-0.2557-0.15410.16520.2759-0.04410.1737-0.276-0.0577-0.020.01540.0544-0.01160.10194.683-0.3097.354
171.42130.38761.3866.8917-0.75112.81770.1847-0.1721-0.2564-0.0018-0.02890.28250.19280.0046-0.1558-0.1056-0.00560.0153-0.05580.017-0.032829.693-3.9516.869
188.72924.7458-8.33339.7408-5.47018.07860.3751-0.7215-0.10.8232-0.32730.3783-0.38990.5624-0.0478-0.0101-0.01640.02510.0020.00520.037110.6770.51219.306
195.61061.4869-0.73483.0832-0.48521.3033-0.04840.0590.0834-0.0805-0.01570.11610.04050.00830.0642-0.1171-0.0054-0.0079-0.0896-0.0007-0.025829.3619.811.077
202.2131-1.41570.02838.3781-1.4841.7644-0.02120.50870.0288-0.25530.19150.35980.0011-0.2287-0.1703-0.1059-0.0256-0.04010.02040.006-0.008311.2130.3684.481
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION1A94 - 99
3X-RAY DIFFRACTION1A6 - 10
4X-RAY DIFFRACTION2B1 - 5
5X-RAY DIFFRACTION2B94 - 99
6X-RAY DIFFRACTION2B6 - 10
7X-RAY DIFFRACTION3A11 - 20
8X-RAY DIFFRACTION4A21 - 32
9X-RAY DIFFRACTION5A33 - 43
10X-RAY DIFFRACTION6B11 - 20
11X-RAY DIFFRACTION7B21 - 32
12X-RAY DIFFRACTION8B33 - 43
13X-RAY DIFFRACTION9A44 - 56
14X-RAY DIFFRACTION10B44 - 56
15X-RAY DIFFRACTION11A57 - 62
16X-RAY DIFFRACTION12A63 - 68
17X-RAY DIFFRACTION13A69 - 76
18X-RAY DIFFRACTION14B57 - 62
19X-RAY DIFFRACTION15B63 - 68
20X-RAY DIFFRACTION16B69 - 76
21X-RAY DIFFRACTION17A77 - 85
22X-RAY DIFFRACTION18B77 - 85
23X-RAY DIFFRACTION19A86 - 93
24X-RAY DIFFRACTION20B86 - 93

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