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- PDB-3ekx: Crystal structure of the wild-type HIV-1 protease with the inhibi... -

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Basic information

Entry
Database: PDB / ID: 3ekx
TitleCrystal structure of the wild-type HIV-1 protease with the inhibitor, Nelfinavir
ComponentsProtease
KeywordsHYDROLASE / HIV protease / protease inhibitors / drug resistance / amprenavir / AIDS / Protease
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 / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / 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 / viral translational frameshifting / 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. / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / 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-1UN / ACETATE ION / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHIV-1 M:B_ARV2/SF2 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsSchiffer, C.A. / Nalam, M.N.L.
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 / Refinement description / Version format compliance
Revision 1.2Oct 17, 2012Group: Database references
Revision 1.3Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)22,2584
Polymers21,6322
Non-polymers6272
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-29 kcal/mol
Surface area8900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.924, 57.848, 61.572
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 / Retropepsin / PR


Mass: 10815.790 Da / Num. of mol.: 2 / Fragment: UNP residues 491-589 / Mutation: Q7K, V64I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_ARV2/SF2 (virus) / Strain: HXB2 / Gene: gag-pol / Plasmid: PXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP106 / References: UniProt: P03369, HIV-1 retropepsin
#2: Chemical ChemComp-1UN / 2-[2-HYDROXY-3-(3-HYDROXY-2-METHYL-BENZOYLAMINO)-4-PHENYL SULFANYL-BUTYL]-DECAHYDRO-ISOQUINOLINE-3-CARBOXYLIC ACID TERT-BUTYLAMIDE / NELFINAVIR MESYLATE AG1343


Mass: 567.782 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H45N3O4S / Comment: medication, antiretroviral, protease inhibitor*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 126mM Sodium Phosphate pH 6.2; 63mM sodium citrate; 24-29% ammonium sulphate , 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 / 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: 1.97→50 Å / Num. obs: 13251 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 22.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F7A

1f7a


Resolution: 1.97→39.25 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.775 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.197 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22999 652 4.9 %RANDOM
Rwork0.184 ---
all0.184 ---
obs0.18627 12557 98.33 %-
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: 33.032 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å20 Å20 Å2
2--1.63 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.97→39.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1490 0 44 118 1652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0221581
X-RAY DIFFRACTIONr_bond_other_d0.0010.021543
X-RAY DIFFRACTIONr_angle_refined_deg1.3272.0132159
X-RAY DIFFRACTIONr_angle_other_deg1.64133580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1475202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.06825.38552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84115257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.493156
X-RAY DIFFRACTIONr_chiral_restr0.0720.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021730
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02280
X-RAY DIFFRACTIONr_nbd_refined0.1840.2224
X-RAY DIFFRACTIONr_nbd_other0.1980.21536
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2746
X-RAY DIFFRACTIONr_nbtor_other0.0850.2931
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.287
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0920.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1870.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.40.29
X-RAY DIFFRACTIONr_mcbond_it0.6571.51293
X-RAY DIFFRACTIONr_mcbond_other0.1231.5422
X-RAY DIFFRACTIONr_mcangle_it0.79121621
X-RAY DIFFRACTIONr_scbond_it1.2243655
X-RAY DIFFRACTIONr_scangle_it1.8684.5538
LS refinement shellResolution: 1.97→2.018 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 53 -
Rwork0.188 785 -
obs--85.51 %
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)
14.8478-2.15060.42122.0723-0.47924.3083-0.1013-0.0053-0.46150.09140.03640.13890.3265-0.03610.0648-0.08190.00020.0152-0.16120.0329-0.106119.946317.992923.5791
25.0302-1.53680.5414.1037-0.21241.9886-0.1879-0.37170.19870.14360.0899-0.1061-0.023-0.08140.098-0.08110.04280.0011-0.0646-0.0065-0.192421.446825.651729.4705
35.143-0.85081.40536.02350.41170.45450.1373-0.0098-0.1639-0.1476-0.0828-0.06880.00570.0654-0.0545-0.05990.00780.0085-0.09330.0146-0.140212.835626.599318.606
45.1541.75641.51853.5450.69862.59230.05370.04080.0232-0.0308-0.1129-0.1012-0.195-0.11320.0593-0.10830.0199-0.0081-0.11440.0249-0.118927.961728.203718.9124
513.5009-2.6041-10.99257.04534.5079.82070.50960.2623-0.4142-0.3611-0.54750.8272-0.0591-0.640.0378-0.1514-0.0016-0.0219-0.1418-0.01810.0132.111221.191718.9431
614.15124.1019-10.506215.7519-3.756313.6753-0.2415-0.36940.07110.0916-0.2977-1.48620.15820.49390.5392-0.14420.008-0.0913-0.18050.10150.02739.295830.373123.6404
710.0009-4.2848-0.778214.02724.8087.03310.33930.2228-0.2641-0.1357-0.31140.39960.3164-0.6051-0.0279-0.1884-0.0448-0.0001-0.11190.0693-0.19630.501133.684913.4882
810.5353-0.9184-1.81354.67194.72219.5424-0.1520.01010.1129-0.06090.1928-0.1113-0.21960.4843-0.0408-0.149-0.0240.0057-0.08240.1244-0.120639.573330.51499.8983
913.4413-0.8512-2.15594.7677-2.50222.30260.12160.0067-0.0727-0.2254-0.06460.02020.11990.1094-0.0569-0.07710.0178-0.0238-0.12750.0103-0.14512.697538.970711.3093
1018.8126-1.3394-3.86752.65970.34975.36560.0146-0.0410.08390.00730.01010.1579-0.18060.0238-0.0248-0.05680.0020.0068-0.111-0.0196-0.165527.208530.70634.6958
117.3407-8.98795.248911.0705-6.04355.98660.40910.70790.0337-0.2543-0.5603-0.04220.14910.59160.1512-0.1194-0.0011-0.0369-0.05250.0378-0.142110.375628.670112.6438
124.51935.2582-7.23396.1784-8.382111.59890.12770.65310.68250.04570.67480.7601-0.054-0.7971-0.8025-0.12170.0130.0022-0.04720.12190.008329.700433.001814.7581
131.947-0.9342-2.085.2252-3.08375.7101-0.2834-0.2772-0.0046-0.05770.44570.13350.2032-0.2196-0.1623-0.08570.02870.0184-0.07310.0143-0.117912.138528.869426.9987
143.2834-0.7361-0.68254.90880.76770.2215-0.17910.2827-0.08430.0634-0.1205-0.0619-0.07650.10540.2996-0.0670.01160.0077-0.07240.0223-0.078629.116819.61619.6274
1511.79336.8832-10.07798.0767-13.401322.54060.3676-0.4160.90070.15110.69110.5905-0.6041-0.5863-1.0587-0.15320.0360.0145-0.12790.0837-0.01861.462436.203320.9949
167.2758-2.98072.181611.3207-12.545126.28520.17550.518-0.823-0.4903-0.5879-0.67070.25470.80110.4124-0.21640.01840.0558-0.08290.0051-0.095739.121923.010910.2831
1742.7455-14.955817.68565.2327-6.18787.31730.64741.23930.443-0.4457-0.97660.02260.67430.40110.3292-0.13310.00730.1119-0.08440.0487-0.01573.856223.433924.646
1820.9318-4.1147-14.04126.5455-3.865717.07190.33570.3860.47870.49060.0286-0.23870.5002-0.5678-0.3643-0.175-0.0498-0.0695-0.1487-0.0398-0.057337.455624.187523.5383
190.30521.3709-1.43097.2032-6.48326.71160.0489-0.19830.0589-0.2630.00160.57110.3210.1978-0.0506-0.11410.0163-0.0094-0.09110.0413-0.06284.483429.537824.9971
203.1023-2.81280.84414.14581.87378.03470.09570.07740.0947-0.1559-0.2399-0.39360.53840.24430.1442-0.1839-0.0423-0.0014-0.10360.0097-0.064336.107621.774117.344
2134.0182-3.6156-1.76451.7892-3.22458.37840.67440.08481.1585-0.1198-0.3503-1.65840.0672-1.3411-0.324-0.1140.00450.0225-0.03310.1162-0.059420.072530.460414.0381
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 DIFFRACTION3A20 - 32
8X-RAY DIFFRACTION4B20 - 32
9X-RAY DIFFRACTION5A11 - 19
10X-RAY DIFFRACTION6B11 - 19
11X-RAY DIFFRACTION7A33 - 43
12X-RAY DIFFRACTION8B33 - 43
13X-RAY DIFFRACTION9A44 - 57
14X-RAY DIFFRACTION10B44 - 57
15X-RAY DIFFRACTION11A77 - 85
16X-RAY DIFFRACTION12B77 - 85
17X-RAY DIFFRACTION13A86 - 93
18X-RAY DIFFRACTION14B86 - 93
19X-RAY DIFFRACTION15A58 - 62
20X-RAY DIFFRACTION16B58 - 62
21X-RAY DIFFRACTION17A63 - 68
22X-RAY DIFFRACTION18B63 - 68
23X-RAY DIFFRACTION19A69 - 76
24X-RAY DIFFRACTION20B69 - 76
25X-RAY DIFFRACTION21B201

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