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- PDB-2qak: HIV-1 PR mutant in complex with nelfinavir -

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Basic information

Entry
Database: PDB / ID: 2qak
TitleHIV-1 PR mutant in complex with nelfinavir
ComponentsPROTEASE RETROPEPSIN
KeywordsHYDROLASE / HIV protease inhibitors / protease-inhibitor structure / isothermal calorimetry / antiviral resistance development
Function / homology
Function and homology information


RNA stem-loop binding / host cell / 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 ...RNA stem-loop binding / host cell / 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 / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / 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 / 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. / 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
Chem-1UN / Gag-Pol polyprotein
Similarity search - Component
Biological specieshuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRezacova, P. / Kozisek, M. / Saskova, K. / Brynda, J. / Konvalinka, J.
CitationJournal: To be Published
Title: Evolutionary pathway of HIV resistance analyzed on molecular level: Enzymatic activities, 3-D structures and thermodynamics of HIV proteases resistant to nelfinavir
Authors: Kozisek, M. / Bray, J. / Rezacova, P. / Saskova, K. / Rulisek, L. / Brynda, J. / Pokorna, J. / Mammano, F. / Konvalinka, J.
History
DepositionJun 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_seq_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEASE RETROPEPSIN
B: PROTEASE RETROPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0933
Polymers21,5252
Non-polymers5681
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-30 kcal/mol
Surface area8920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.500, 62.500, 82.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPHEPHEAA1 - 991 - 99
21PROPROPHEPHEBB1 - 991 - 99
121UN1UN1UN1UNAC1001

NCS ensembles :
ID
1
2
Detailsthe biological assembly is dimer

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Components

#1: Protein PROTEASE RETROPEPSIN / E.C.3.4.23.16 / HIV-1 PROTEASE


Mass: 10762.707 Da / Num. of mol.: 2 / Mutation: D30N, L90M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) human immunodeficiency virus 1 / Strain: type B / Gene: gag-pol / Plasmid: pET like, T7 promotor driven / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P03367, 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 / Nelfinavir


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


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.15 Å3/Da / Density % sol: 42.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: reservoir solution: 0.5M (NH4)2SO4, 0.1M MES pH 5.4 or pH 5.5; drops: 2+1ul (protein+reservoir}; protein: 3-5mg/ml 5-fold molar excess of inhibitor, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 3, 2005
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.2→54.23 Å / Num. all: 8471 / Num. obs: 8471 / % possible obs: 95.93 % / Redundancy: 7.1 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 6.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1177 / Rsym value: 0.377 / % possible all: 87.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NH0

1nh0


Resolution: 2.2→54.23 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.921 / Cross valid method: THROUGHOUT / ESU R: 0.462 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23603 430 4.8 %RANDOM
Rwork0.2033 ---
obs0.20491 8471 95.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.877 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.13 Å20 Å2
2--0.27 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→54.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 80 100 1696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221631
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5782.0362221
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9645198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.49525.27355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78215276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.464156
X-RAY DIFFRACTIONr_chiral_restr0.0940.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021164
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.2758
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21086
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.287
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6671.5981
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.13121594
X-RAY DIFFRACTIONr_scbond_it1.7873650
X-RAY DIFFRACTIONr_scangle_it2.5934.5626
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1749medium positional0.240.5
240medium positional0.070.5
1749medium thermal0.542
240medium thermal0.262
LS refinement shellResolution: 2.2→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 21 -
Rwork0.297 505 -
obs--78.04 %
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)
10.34040.90860.92113.9875-0.28227.29660.17990.16340.0709-0.0157-0.1978-0.7298-0.43710.71250.018-0.0935-0.00490.0111-0.07220.021-0.01751.27556.9342.641
20.7775-0.53471.09958.6863-3.07753.4263-0.03020.10880.1527-0.20760.0267-0.1326-0.03010.13860.0035-0.12750.00650.0083-0.16850.0052-0.1438-6.73563.438-4.973
39.01442.4739-4.48117.4171-2.56238.8296-0.19510.81110.1281-1.030.51610.66240.7158-1.0304-0.3210.012-0.0685-0.13820.02690.05940.002-17.01959.482-10.135
40.05190.206-0.61175.3182-0.13538.38060.0708-0.0911-0.1930.0217-0.1558-0.79470.19380.71930.085-0.12590.02270.0041-0.0799-0.0072-0.02311.3551.3545.567
50.2135-0.0794-0.719610.224-3.96324.18170.0169-0.1075-0.1370.3205-0.0165-0.1897-0.03640.1158-0.0004-0.1397-0.0027-0.0123-0.16920.0027-0.15-6.74844.83812.977
67.0818-2.3311.57767.156-3.26078.5336-0.2538-0.6895-0.22860.89610.54960.7041-0.6045-1.0448-0.29580.0170.080.11550.06720.03040.0266-17.12448.77618.438
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 91 - 9
2X-RAY DIFFRACTION1AA86 - 9986 - 99
3X-RAY DIFFRACTION2AA10 - 3210 - 32
4X-RAY DIFFRACTION2AA63 - 8563 - 85
5X-RAY DIFFRACTION3AA33 - 6233 - 62
6X-RAY DIFFRACTION4BB1 - 91 - 9
7X-RAY DIFFRACTION4BB86 - 9986 - 99
8X-RAY DIFFRACTION5BB10 - 3210 - 32
9X-RAY DIFFRACTION5BB63 - 8563 - 85
10X-RAY DIFFRACTION6BB33 - 6233 - 62

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