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- PDB-3ekt: Crystal Structure of the inhibitor Darunavir (DRV) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3ekt
TitleCrystal Structure of the inhibitor Darunavir (DRV) in complex with a multi-drug resistant HIV-1 protease variant (L10F/G48V/I54V/V64I/V82A) (Refer: FLAP+ in citation.)
ComponentsProtease
KeywordsHYDROLASE / HIV-1 / protease / multi-drug resistance / Darunavir / AIDS
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / host multivesicular body / viral penetration into host nucleus / 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 / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / 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 / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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-017 / ACETATE ION / PHOSPHATE ION / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHIV-1 M:B_ARV2/SF2 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 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: Non-polymer description / Version format compliance
Revision 1.2Jul 25, 2012Group: Data collection / Database references
Revision 1.3Oct 17, 2012Group: Database references
Revision 1.4Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.5Oct 20, 2021Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_unobs_or_zero_occ_residues / 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
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
C: Protease
D: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,30619
Polymers43,2634
Non-polymers2,04315
Water5,783321
1
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3566
Polymers21,6322
Non-polymers7254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-35 kcal/mol
Surface area9030 Å2
MethodPISA
2
C: Protease
D: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,94913
Polymers21,6322
Non-polymers1,31811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-67 kcal/mol
Surface area9150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.013, 92.013, 106.161
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Protease / Retropepsin / PR


Mass: 10815.788 Da / Num. of mol.: 4 / 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#3: 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*YM
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 3 Å3/Da / Density % sol: 58.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: Refer citation, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.97→40 Å / Num. all: 34578 / Num. obs: 34578 / % possible obs: 95.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.2.0005refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→40 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.899 / Occupancy max: 1 / Occupancy min: 0 / SU B: 6.766 / SU ML: 0.133 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1713 5 %RANDOM
Rwork0.209 ---
obs0.211 34447 95.59 %-
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: 53.77 Å2 / Biso mean: 13.827 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20.19 Å20 Å2
2--0.39 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.97→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2948 0 133 321 3402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223295
X-RAY DIFFRACTIONr_bond_other_d0.0010.023170
X-RAY DIFFRACTIONr_angle_refined_deg1.122.0284521
X-RAY DIFFRACTIONr_angle_other_deg1.0637350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.675422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.76125104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93815507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7161514
X-RAY DIFFRACTIONr_chiral_restr0.0740.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023612
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02585
X-RAY DIFFRACTIONr_nbd_refined0.1950.3549
X-RAY DIFFRACTIONr_nbd_other0.2240.33229
X-RAY DIFFRACTIONr_nbtor_refined0.1810.51561
X-RAY DIFFRACTIONr_nbtor_other0.0870.51851
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.5374
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1820.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.316
X-RAY DIFFRACTIONr_symmetry_vdw_other0.20.369
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2550.539
X-RAY DIFFRACTIONr_mcbond_it0.8971.52673
X-RAY DIFFRACTIONr_mcbond_other0.1161.5858
X-RAY DIFFRACTIONr_mcangle_it0.98723363
X-RAY DIFFRACTIONr_scbond_it1.71131370
X-RAY DIFFRACTIONr_scangle_it2.4244.51158
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 151 -
Rwork0.215 2400 -
all-2551 -
obs--97 %
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)
12.894-0.19323.97751.18711.29977.55320.17060.1286-0.14120.04850.0075-0.03010.22290.1672-0.1781-0.07310.0054-0.007-0.05750.0027-0.063122.8694-35.421635.5564
22.02250.67364.24334.03641.67599.28720.1575-0.0708-0.1550.15830.0531-0.11730.30830.0062-0.2106-0.0588-0.0026-0.0022-0.1023-0.0034-0.070919.2128-37.525935.2454
316.70125.7972-3.33472.5708-1.17731.45710.13680.29970.17550.0949-0.03730.1890.0031-0.0039-0.0994-0.0915-0.0276-0.0033-0.00070.0152-0.069116.5673-26.106930.8624
412.26810.3004-2.52849.523-2.32240.56660.19930.03670.32520.262-0.22450.1219-0.0944-0.07170.0252-0.0279-0.04840.0172-0.0592-0.007-0.051714.3363-27.379839.9495
54.6007-4.04380.85163.5622-0.353820.06320.12810.37530.05270.087-0.1807-0.1141-0.3508-0.35890.0525-0.1461-0.0037-0.04220.0226-0.0152-0.02286.0024-16.456227.0424
60.5979-1.64360.02094.63521.577622.77310.06650.06640.05510.2829-0.01490.1955-0.5157-0.2968-0.0516-0.0017-0.0757-0.0401-0.1132-0.0249-0.045611.0356-13.376243.4069
721.6544-9.41939.20499.0381-10.034615.47910.46040.1458-0.3804-0.0836-0.04260.08570.2072-0.7042-0.4177-0.0793-0.09290.0121-0.0443-0.0315-0.139919.4115-26.417716.8184
86.35290.1302-3.368517.57995.62038.48030.0854-0.0503-0.20220.374-0.0027-0.2024-0.49520.3885-0.0826-0.1437-0.0484-0.0199-0.00380.0303-0.145313.1811-29.987253.9893
914.5014-6.86194.96169.4153-4.257911.0026-0.41530.8981-0.4274-0.34970.0789-0.15280.83530.09430.3364-0.0144-0.09360.071-0.1116-0.0215-0.025923.0795-31.877217.3412
105.83974.51251.5369.20492.72968.63870.3144-0.8123-0.27930.1465-0.8145-0.38370.22270.30270.5001-0.1708-0.0238-0.00280.02640.10930.006216.0479-35.893853.4542
118.1682-1.601-0.68722.0504-1.35481.84040.12710.08810.93120.103-0.1864-0.4485-0.1313-0.37310.0593-0.1008-0.0130.0089-0.03110.080.008915.2999-19.036425.4039
125.44540.3186-0.41887.3944-0.79551.2452-0.00550.21370.18970.2430.01790.8797-0.31630.106-0.0124-0.074-0.03760.0786-0.0909-0.0264-0.00348.8339-22.773745.3862
135.3457-5.0818-2.25364.88742.67235.92690.1020.3958-0.0988-0.1745-0.023-0.0761-0.0323-0.0463-0.079-0.0273-0.0481-0.0123-0.02450.0211-0.015215.9039-31.993325.3158
140.948-2.24032.40518.8238-3.86257.0410.0567-0.0212-0.14680.32950.0389-0.28480.01040.0192-0.0957-0.0902-0.02160.01650.0278-0.0075-0.021219.759-29.786445.5326
152.21443.8964-0.432612.4958-5.19743.5740.0424-0.05870.3264-0.2012-0.02560.4193-0.2065-0.381-0.0167-0.12690.0199-0.01730.0045-0.00190.0153.132249.4202-10.1434
169.56418.1082-4.24499.3961-1.75793.22750.0583-0.33860.2050.0438-0.18890.4598-0.335-0.31740.1306-0.0620.0711-0.011-0.080.00350.02584.757752.2701-7.5197
174.52221.33542.63693.70075.62648.64530.1290.1013-0.22720.07090.0868-0.2043-0.0994-0.0218-0.2158-0.02060.0142-0.00280.00070.0193-0.03515.083947.4723-12.6988
181.8829-0.08882.87311.95371.91526.5410.06270.0903-0.0819-0.0863-0.0106-0.2635-0.1009-0.177-0.052-0.02850.01370.0027-0.02460.0152-0.013712.439442.9146-4.9603
193.05482.765-5.4844.4081-8.408216.0718-0.3977-0.2798-0.1082-0.252-0.0187-0.43390.01050.46470.4164-0.10550.0975-0.02840.0077-0.0696-0.002929.622445.4591-11.525
201.61261.9598-4.55288.0992-10.033416.39640.07340.0701-0.32060.044-0.4935-0.40210.36140.14460.4201-0.11020.0944-0.06020.0014-0.061-0.015821.617330.959-5.9849
2131.31213.83334.01310.56424.93527.9667-0.57980.42930.157-0.26190.22950.0413-0.99050.00220.35020.05540.04140.0775-0.18820.0031-0.123618.313456.4986-23.3073
224.0843-6.51270.738145.63036.70698.45210.0771-0.0956-0.13580.6723-0.44880.08540.5678-0.85750.3717-0.1512-0.083-0.0551-0.00980.0604-0.13576.243835.58825.6682
2342.904524.51839.696920.4726-1.834610.6119-0.7322-0.06-0.0811-0.76960.82080.1837-0.9736-0.1301-0.08870.1140.1427-0.0039-0.1331-0.0533-0.087612.052958.453-22.8263
248.4342-5.2094-6.166891.2591.18154.58730.4802-0.1646-0.20561.499-0.3081.13080.4285-0.6834-0.1722-0.1556-0.0696-0.06190.1766-0.0275-0.07481.14240.07815.8561
252.62860.9588-0.04294.26732.01011.04820.124-0.03480.09710.0027-0.0418-0.06540.13320.2402-0.0822-0.0239-0.0008-0.003-0.057-0.032-0.052622.291946.3358-17.935
263.7910.44382.64892.98061.38182.2430.06440.1752-0.0072-0.21650.04460.0650.26430.1775-0.1089-0.02-0.0131-0.0148-0.0321-0.0151-0.06417.022337.22280.2661
272.2881-3.04521.32436.261-0.15281.94010.3740.13950.2691-0.3803-0.0677-0.0258-0.2154-0.0144-0.30630.0385-0.00340.013-0.07980.0098-0.018714.238655.2591-13.8044
289.41841.60850.5440.28810.02910.3360.1301-0.5688-0.32680.06230.17980.19320.2259-0.0316-0.3099-0.0189-0.03510.0032-0.01580.0072-0.02745.280239.7089-3.8502
2917.7671-3.53487.96815.61113.093733.4429-0.2365-0.4319-0.2636-0.5730.4824-0.0076-0.9269-0.4616-0.2459-0.01530.0098-0.0053-0.09060.00450.007412.2388-21.13235.4023
3022.87913.5410.458441.24836.47521.1673-0.18251.03550.220.92960.59650.78250.06510.8535-0.4140.03670.037-0.02180.20420.0582-0.017418.961941.3557-9.2086
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION1A94 - 99
3X-RAY DIFFRACTION2B1 - 5
4X-RAY DIFFRACTION2B94 - 99
5X-RAY DIFFRACTION3A22 - 30
6X-RAY DIFFRACTION4B22 - 30
7X-RAY DIFFRACTION5A44 - 57
8X-RAY DIFFRACTION6B44 - 57
9X-RAY DIFFRACTION7A60 - 66
10X-RAY DIFFRACTION8B60 - 66
11X-RAY DIFFRACTION9A68 - 72
12X-RAY DIFFRACTION10B68 - 72
13X-RAY DIFFRACTION11A74 - 85
14X-RAY DIFFRACTION12B74 - 85
15X-RAY DIFFRACTION13A86 - 93
16X-RAY DIFFRACTION14B86 - 93
17X-RAY DIFFRACTION15C1 - 5
18X-RAY DIFFRACTION15C94 - 99
19X-RAY DIFFRACTION16D1 - 5
20X-RAY DIFFRACTION16D94 - 99
21X-RAY DIFFRACTION17C22 - 30
22X-RAY DIFFRACTION18D22 - 30
23X-RAY DIFFRACTION19C44 - 57
24X-RAY DIFFRACTION20D44 - 57
25X-RAY DIFFRACTION21C60 - 66
26X-RAY DIFFRACTION22D60 - 66
27X-RAY DIFFRACTION23C68 - 72
28X-RAY DIFFRACTION24D68 - 72
29X-RAY DIFFRACTION25C74 - 85
30X-RAY DIFFRACTION26D74 - 85
31X-RAY DIFFRACTION27C86 - 93
32X-RAY DIFFRACTION28D86 - 93
33X-RAY DIFFRACTION29D - P200
34X-RAY DIFFRACTION30Q200

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Yorodumi

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  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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