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- PDB-3r4b: Crystal Structure of Wild-type HIV-1 Protease in Complex With TMC... -

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Basic information

Entry
Database: PDB / ID: 3r4b
TitleCrystal Structure of Wild-type HIV-1 Protease in Complex With TMC310911
ComponentsHIV-1 protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / drug resistance / drug design / protease inhibitors / AIDS / aspartyl protease / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


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 ...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 / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / endonuclease activity / 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 / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA 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
(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl / PHOSPHATE ION / Gag-Pol polyprotein / Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSchiffer, C.A. / Nalam, M.N.L.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2011
Title: TMC310911, a Novel Human Immunodeficiency Virus Type 1 Protease Inhibitor, Shows In Vitro an Improved Resistance Profile and Higher Genetic Barrier to Resistance Compared with Current Protease Inhibitors.
Authors: Dierynck, I. / Van Marck, H. / Van Ginderen, M. / Jonckers, T.H. / Nalam, M.N. / Schiffer, C.A. / Raoof, A. / Kraus, G. / Picchio, G.
History
DepositionMar 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 protease
B: HIV-1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4834
Polymers21,6322
Non-polymers8512
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-28 kcal/mol
Surface area9210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.681, 58.369, 61.116
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 HIV-1 protease /


Mass: 10815.790 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: HXB2 / Gene: gag-pol, pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP106 / References: UniProt: Q90K99, UniProt: P03369*PLUS
#2: Chemical ChemComp-74T / (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl {(2S,3R)-4-[({2-[(1-cyclopentylpiperidin-4-yl)amino]-1,3-benzothiazol-6-yl}sulfonyl)(2-methylpropyl)amino]-3-hydroxy-1-p henylbutan-2-yl}carbamate / TMC310911


Mass: 755.987 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H53N5O7S2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 41.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 24-29% ammonium sulfate, 63 mM sodium citrate, 126 mM phosphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 9, 2005
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 14669 / % possible obs: 98.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.054 / Χ2: 1.016 / Net I/σ(I): 13.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.975.90.32314121.029196.5
1.97-2.056.60.26714171.083197.5
2.05-2.146.70.20414171197.9
2.14-2.256.70.14614260.96197.8
2.25-2.396.70.11614561.001198.9
2.39-2.586.80.09114590.977198.7
2.58-2.846.80.07114671.046199.4
2.84-3.256.70.05114931.062199.6
3.25-4.096.80.03715110.9641100
4.09-506.50.02716111.044199.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F7A

1f7a


Resolution: 1.9→42.22 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.2217 / WRfactor Rwork: 0.1751 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8406 / SU B: 7.484 / SU ML: 0.113 / SU R Cruickshank DPI: 0.18 / SU Rfree: 0.1583 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 738 5 %RANDOM
Rwork0.1794 ---
obs0.1818 14635 98.67 %-
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 max: 74.97 Å2 / Biso mean: 39.0945 Å2 / Biso min: 23.71 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å20 Å2
2---0.18 Å20 Å2
3---1.68 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1494 0 57 96 1647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221746
X-RAY DIFFRACTIONr_bond_other_d0.0010.021184
X-RAY DIFFRACTIONr_angle_refined_deg1.5272.0562399
X-RAY DIFFRACTIONr_angle_other_deg0.80832929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3495218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.462560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17915280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.181159
X-RAY DIFFRACTIONr_chiral_restr0.0820.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211895
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02314
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 57 -
Rwork0.198 976 -
all-1033 -
obs--95.65 %
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)
14.7765-3.2275-0.18483.5637-0.25183.7197-0.0977-0.0031-0.32170.21480.08110.32280.1797-0.04980.01660.0723-0.00590.03630.0350.02360.064519.826517.638122.905
26.84460.2985-0.96352.95421.89152.0649-0.0147-0.44180.20490.1137-0.01520.104-0.0525-0.05410.02990.13650.03590.01530.1287-0.01930.011320.963125.814229.1044
35.5896-1.29550.54574.8416-1.09262.59170.0443-0.0803-0.2272-0.04840.07980.34790.0427-0.1708-0.12410.04090.00110.03160.02240.00320.129413.958427.582318.794
44.43771.74151.88885.6166-1.58261.9179-0.1123-0.02390.03230.03810.0046-0.1167-0.1089-0.0160.10760.04150.007-0.01370.061-0.01110.041326.501427.568318.3433
521.459-5.8358-2.36542.45-1.88657.68460.44130.8659-0.8245-0.0269-0.04790.3824-0.3118-0.7116-0.39350.1117-0.0023-0.00770.1856-0.05270.37921.371721.961216.9368
66.00364.5673-0.95138.826-0.91486.02240.1355-0.0953-0.23050.1188-0.2488-0.9086-0.22040.50260.11330.0936-0.0129-0.0750.12680.06620.180839.245431.184523.2405
79.17161.3745-2.00515.08061.43943.03910.19390.46860.15180.0098-0.0541-0.03060.2287-0.4045-0.13980.14110.0091-0.01020.1980.07960.1580.278334.525712.9471
87.05022.04941.71571.42892.04994.65770.05340.12420.0049-0.16220.0091-0.1719-0.1310.2965-0.06250.15330.0090.01640.13380.07460.1339.505831.07119.2359
919.4931-11.3915-1.664812.4193-0.97080.98720.01450.0685-0.00230.29150.05470.4538-0.1182-0.0457-0.06920.105-0.01550.01910.083-0.00390.071713.785140.150411.3304
1014.4173-0.6096-3.89090.05310.47494.57950.02150.3216-0.29460.0023-0.00720.00450.04120.0232-0.01430.07940.01380.01190.02710.00120.045325.894131.13633.8735
1110.3278-8.18887.211513.5761-11.24489.56610.82890.5706-0.6836-0.7665-0.42290.80340.57940.475-0.4060.16140.0339-0.13560.12760.02370.313410.653129.680511.7389
120.96961.5752-2.94084.8959-2.568711.12870.16790.06830.11290.0510.02720.3851-0.8071-0.1901-0.19510.1118-0.0002-0.02070.10370.01120.091329.187633.52114.1427
138.1578-3.6595-4.56591.88231.42594.1946-0.3672-0.6177-0.30260.19370.39980.23240.09170.037-0.03260.12950.03980.01920.13370.05610.200611.965229.106226.786
143.90780.87512.65473.5909-0.35842.72970.03040.082-0.24120.02310.03560.03370.00790.1012-0.06590.05160.00160.00920.0497-0.00550.04728.762719.512719.0706
157.71887.6663-9.93112.3176-14.285119.59870.4163-0.0670.37890.2070.18450.366-0.243-0.0841-0.60080.11840.07560.03140.15280.03750.33281.846337.071718.5133
164.0187-5.11513.934210.9155-14.070122.517100.1525-0.2728-0.0696-0.567-0.08690.10410.87550.5670.0590.02470.03950.18040.01570.168638.491325.48559.0416
1715.0695-16.1382-0.921918.6094-0.266211.3347-0.20830.30170.65640.253-0.0381-1.03080.53310.54650.24640.1110.05420.03190.18440.02310.25452.908223.171823.9452
1814.8866-2.2476-1.07425.72613.411215.16-0.25970.03970.54440.48860.113-0.2570.3060.03340.14670.0907-0.0107-0.0680.01650.0150.180537.53424.359223.9731
190.86141.1816-1.84228.6622-6.07657.6409-0.0282-0.17650.27250.03490.19790.20050.22680.0925-0.16970.08930.03690.02310.16180.00560.23254.110728.710825.0408
201.26260.14711.13013.3352-2.67446.6854-0.1267-0.012-0.04130.0982-0.1478-0.28530.01990.09020.27450.0664-0.00020.01620.09410.01210.087135.78221.923617.9443
212.78960.3281-0.8833.49421.728610.9791-0.0997-0.20640.02360.21070.30380.18580.02610.3713-0.20410.06760.03510.01120.11380.03090.091420.210731.085813.6511
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 DIFFRACTION3A21 - 32
8X-RAY DIFFRACTION4B21 - 32
9X-RAY DIFFRACTION5A11 - 20
10X-RAY DIFFRACTION6B11 - 20
11X-RAY DIFFRACTION7A33 - 43
12X-RAY DIFFRACTION8B33 - 43
13X-RAY DIFFRACTION9A44 - 56
14X-RAY DIFFRACTION10B44 - 56
15X-RAY DIFFRACTION11A77 - 85
16X-RAY DIFFRACTION12B77 - 85
17X-RAY DIFFRACTION13A86 - 93
18X-RAY DIFFRACTION14B86 - 93
19X-RAY DIFFRACTION15A57 - 62
20X-RAY DIFFRACTION16B57 - 62
21X-RAY DIFFRACTION17A63 - 68
22X-RAY DIFFRACTION18B63 - 68
23X-RAY DIFFRACTION19A69 - 76
24X-RAY DIFFRACTION20B69 - 76
25X-RAY DIFFRACTION21A200

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