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- PDB-3el0: Crystal structure of the inhibitor Nelfinavir (NFV) in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3el0
TitleCrystal structure of the inhibitor Nelfinavir (NFV) in complex with a multi-drug resistant HIV-1 protease variant (L10I/G48V/I54V/V64I/V82A) (Refer: FLAP+ in citation)
ComponentsProtease
KeywordsHYDROLASE / HIV-1 / protease / multi-drug resistance / Nelfinavir / 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 / viral translational frameshifting / 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 / 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-1UN / ACETATE ION / PHOSPHATE ION / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHIV-1 M:B_ARV2/SF2 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsPrabu-Jeyabalan, M. / King, N.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 1.2Oct 17, 2012Group: Database references
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)22,68510
Polymers21,6322
Non-polymers1,0538
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-36 kcal/mol
Surface area9410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.073, 58.484, 61.096
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-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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.11 Å3/Da / Density % sol: 41.68 %
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: Apr 12, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 12125 / Num. obs: 12125 / Rmerge(I) obs: 0.044 / Net I/σ(I): 12.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT3.006data extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementResolution: 2→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 0.1 / SU B: 6.757 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 591 4.9 %RANDOM
Rwork0.197 ---
obs0.2 12104 94.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.88 Å2 / Biso mean: 29.943 Å2 / Biso min: 16.41 Å2
Baniso -1Baniso -2Baniso -3
1--2.92 Å20 Å20 Å2
2--0.37 Å20 Å2
3---2.56 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1483 0 70 125 1678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221609
X-RAY DIFFRACTIONr_bond_other_d0.0050.021563
X-RAY DIFFRACTIONr_angle_refined_deg1.1662.0222191
X-RAY DIFFRACTIONr_angle_other_deg1.27133623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7055202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.17924.46456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1815265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3561510
X-RAY DIFFRACTIONr_chiral_restr0.0680.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021760
X-RAY DIFFRACTIONr_gen_planes_other0.0340.02291
X-RAY DIFFRACTIONr_nbd_refined0.2920.2219
X-RAY DIFFRACTIONr_nbd_other0.2070.21483
X-RAY DIFFRACTIONr_nbtor_refined0.1630.2728
X-RAY DIFFRACTIONr_nbtor_other0.0850.2922
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.260.295
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3310.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.216
X-RAY DIFFRACTIONr_mcbond_it0.9311.51307
X-RAY DIFFRACTIONr_mcbond_other0.1161.5416
X-RAY DIFFRACTIONr_mcangle_it0.97821632
X-RAY DIFFRACTIONr_scbond_it1.5833668
X-RAY DIFFRACTIONr_scangle_it2.2424.5559
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 43 -
Rwork0.241 790 -
all-833 -
obs--89 %
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)
12.77341.19840.69031.46241.39641.75380.07240.24450.1846-0.1425-0.08520.0509-0.1545-0.04490.0127-0.03240.0045-0.0249-0.00910.0148-0.033320.10488.55162.1228
21.6542-1.2167-0.37881.6389-0.0470.2292-0.1341-0.1123-0.0642-0.06880.04150.0238-0.2553-0.04930.0926-0.0484-0.0150.00250.0170.0076-0.005725.12064.015512.9456
36.9516-1.2847-3.13464.29541.41471.607-0.2204-0.0493-0.2134-0.24260.18930.11010.1526-0.00320.0311-0.0641-0.0126-0.0122-0.0117-0.0026-0.01315.11020.07319.9565
414.75036.1423-0.99474.34270.9611.1266-0.09-0.23280.0251-0.14260.00660.38950.026-0.22210.0834-0.04480.0020.0253-0.01330.0167-0.01226.5564-1.240627.0442
56.10341.47970.21885.33750.04092.9569-0.0399-0.19540.08550.09580.0780.3517-0.08760.2085-0.0382-0.0913-0.0230.0081-0.01760.0232-0.024215.25-10.681119.5318
60.2598-1.15940.11995.2043-0.21353.35270.15640.0239-0.2189-0.01580.10030.52830.0887-0.1328-0.2567-0.029-0.025-0.00750.05110.0370.047929.8425-5.132417.1263
71.07310.2479-0.51975.4853-4.48085.40860.0922-0.5609-0.01680.8235-0.34220.1286-0.62450.50070.25-0.0016-0.03240.00720.11080.03290.043810.8898-1.023920.0446
85.0711-0.0973-0.5572.34631.43210.923-0.1131-0.09590.18250.08740.1038-0.12150.0059-0.01020.0092-0.03160.0052-0.01270.0098-0.0163-0.010328.51149.253711.5786
91.8261-1.0276-2.20953.95840.49862.8375-0.07060.2158-0.20410.03550.09150.02780.0584-0.1435-0.021-0.0673-0.0136-0.03150.0185-0.01130.010111.7585-0.65274.7563
105.42499.26722.160817.69381.46713.51580.081-0.48710.28020.2841-0.0388-0.1617-0.0165-0.3707-0.0422-0.0581-0.0190.00240.02320.0170.007520.3187-1.214417.1993
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION1B1 - 5
3X-RAY DIFFRACTION1A94 - 99
4X-RAY DIFFRACTION1B94 - 99
5X-RAY DIFFRACTION2A24 - 31
6X-RAY DIFFRACTION3B24 - 31
7X-RAY DIFFRACTION4A44 - 55
8X-RAY DIFFRACTION5B44 - 55
9X-RAY DIFFRACTION6A77 - 84
10X-RAY DIFFRACTION7B77 - 84
11X-RAY DIFFRACTION8A86 - 92
12X-RAY DIFFRACTION9B86 - 92
13X-RAY DIFFRACTION10A201

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