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- PDB-3kt5: Crystal Structure of N88S mutant HIV-1 Protease -

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Basic information

Entry
Database: PDB / ID: 3kt5
TitleCrystal Structure of N88S mutant HIV-1 Protease
ComponentsProtease
KeywordsHYDROLASE / Drug Resistant / Mutation / HIV-1 protease / N88S / Nelfinavir / Protease
Function / homology
Function and homology information


integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / : / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / protein processing / host multivesicular body / 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 / peptidase activity / 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 / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding
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. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / 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
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.801 Å
AuthorsBihani, S.C. / Das, A. / Prashar, V. / Ferrer, J.L. / Hosur, M.V.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Resistance mechanism revealed by crystal structures of unliganded nelfinavir-resistant HIV-1 protease non-active site mutants N88D and N88S.
Authors: Bihani, S.C. / Das, A. / Prashar, V. / Ferrer, J.L. / Hosur, M.V.
History
DepositionNov 24, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 23, 2017Group: Advisory / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Revision 1.3Nov 10, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease


Theoretical massNumber of molelcules
Total (without water)21,7891
Polymers21,7891
Non-polymers00
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.170, 62.170, 83.000
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 /


Mass: 21788.594 Da / Num. of mol.: 1 / Mutation: N88S, C95A, N1088S, C1095A
Source method: isolated from a genetically manipulated source
Details: The fusion protein of two same subunits (UNP residues 489-587) and linker peptide GGSSG. Two subunits are linked through the linker.
Source: (gene. exp.) Human immunodeficiency virus type 1 / Gene: gag-pol / Plasmid: pET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04585
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE TWO SUBUNITS ARE LINKED THROUGH THE LINKER PEPTIDE OF SEQUENCE GGSSG CONNECTING RESIDUES 99 TO 1001.

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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: 2.13 Å3/Da / Density % sol: 42.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 1-5% saturated Ammonium Sulfate, 200/100mM Phosphate/Citrate Buffer, pH 6.2, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97618 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97618 Å / Relative weight: 1
ReflectionResolution: 1.801→32.869 Å / Num. all: 16879 / Num. obs: 16807 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 20.85 Å2 / Rmerge(I) obs: 0.067
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 5.45 % / Rmerge(I) obs: 0.537 / Num. unique all: 2695 / % possible all: 99

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.801→32.869 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.225 841 5.01 %Random
Rwork0.178 ---
obs0.18 16801 99.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.838 Å2 / ksol: 0.386 e/Å3
Displacement parametersBiso max: 86.15 Å2 / Biso mean: 29.353 Å2 / Biso min: 8.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.314 Å20 Å2-0 Å2
2--0.314 Å2-0 Å2
3----0.628 Å2
Refinement stepCycle: LAST / Resolution: 1.801→32.869 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1588 0 0 241 1829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071629
X-RAY DIFFRACTIONf_angle_d1.1182234
X-RAY DIFFRACTIONf_chiral_restr0.074272
X-RAY DIFFRACTIONf_plane_restr0.007283
X-RAY DIFFRACTIONf_dihedral_angle_d18.67635
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.801-1.9140.2631400.2232655279599
1.914-2.0620.2791390.20826472786100
2.062-2.2690.2751400.19926522792100
2.269-2.5980.2091410.19126772818100
2.598-3.2720.2251400.17526632803100
3.272-32.8750.1941410.1522666280799
Refinement TLS params.Method: refined / Origin x: -11.7176 Å / Origin y: 20.2402 Å / Origin z: 27.6246 Å
111213212223313233
T0.0872 Å2-0.0079 Å2-0.009 Å2-0.099 Å2-0.0055 Å2--0.0799 Å2
L1.1637 °20.1975 °20.6607 °2-0.994 °20.4273 °2--0.5263 °2
S0.0383 Å °0.0289 Å °-0.0189 Å °0.0249 Å °0.0212 Å °-0.0109 Å °0.0704 Å °0.054 Å °0.0028 Å °
Refinement TLS groupSelection details: chain A

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