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- PDB-2o4k: Crystal Structure of HIV-1 Protease (Q7K) in Complex with Atazanavir -

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Basic information

Entry
Database: PDB / ID: 2o4k
TitleCrystal Structure of HIV-1 Protease (Q7K) in Complex with Atazanavir
Componentsprotease
KeywordsVIRAL PROTEIN / protease complex
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 / viral penetration into host nucleus / symbiont-mediated suppression of host gene expression / RNA stem-loop binding / 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 / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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 / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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-DR7 / Gag-Pol polyprotein / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsArmstrong, A.A. / Muzammil, S. / Jakalian, A. / Bonneau, P.R. / Schmelmer, V. / Freire, E. / Amzel, L.M.
CitationJournal: J.Virol. / Year: 2007
Title: Unique thermodynamic response of tipranavir to human immunodeficiency virus type 1 protease drug resistance mutations.
Authors: Muzammil, S. / Armstrong, A.A. / Kang, L.W. / Jakalian, A. / Bonneau, P.R. / Schmelmer, V. / Amzel, L.M. / Freire, E.
History
DepositionDec 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _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
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: protease
B: protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3504
Polymers21,6102
Non-polymers7402
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-44 kcal/mol
Surface area9470 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.741, 85.805, 46.242
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein protease


Mass: 10804.808 Da / Num. of mol.: 2 / Mutation: Q7K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: Subtype B / Gene: gag-pol / Plasmid: pET24 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03367, UniProt: Q903J0*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-DR7 / (3S,8S,9S,12S)-3,12-BIS(1,1-DIMETHYLETHYL)-8-HYDROXY-4,11-DIOXO-9-(PHENYLMETHYL)-6-[[4-(2-PYRIDINYL)PHENYL]METHYL]-2,5, 6,10,13-PENTAAZATETRADECANEDIOIC ACID DIMETHYL ESTER / ATAZANAVIR / METHYL [(1S,4S,5S,10S)-4-BENZYL-1,10-DI-TERT-BUTYL-5-HYDROXY-2,9,12-TRIOXO-7-(4-PYRIDIN-2-YLBENZYL)-13-OXA-3,7,8,11-TETRAAZATET RADEC-1-YL]CARBAMATE


Mass: 704.855 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H52N6O7 / Comment: medication, antiretroviral*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.69 Å3/Da / Density % sol: 54.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.6
Details: 750 mM NaCl, 100 mM citrate buffer, pH 5.6, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 11, 2004 / Details: Osmic Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 30983 / % possible obs: 98.3 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Χ2: 1.201 / Net I/σ(I): 13.9
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 2.88 / Num. unique all: 2968 / Rsym value: 0.472 / Χ2: 1.717 / % possible all: 95.7

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Phasing

Phasing MRRfactor: 0.458 / Cor.coef. Fo:Fc: 0.485
Highest resolutionLowest resolution
Rotation3 Å23.82 Å
Translation3 Å23.82 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MSM

1msm


Resolution: 1.6→23.82 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.476 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.209 3104 10 %RANDOM
Rwork0.183 ---
obs0.186 30961 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.304 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2---0.09 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.6→23.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 52 258 1826
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221680
X-RAY DIFFRACTIONr_angle_refined_deg1.4372.0582284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0425202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.30324.61552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.5215294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.521158
X-RAY DIFFRACTIONr_chiral_restr0.0820.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021212
X-RAY DIFFRACTIONr_nbd_refined0.1920.2777
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21155
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2169
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.215
X-RAY DIFFRACTIONr_mcbond_it0.7811.51037
X-RAY DIFFRACTIONr_mcangle_it1.10121628
X-RAY DIFFRACTIONr_scbond_it1.9173732
X-RAY DIFFRACTIONr_scangle_it2.7484.5656
LS refinement shellResolution: 1.601→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 211 -
Rwork0.382 1907 -
obs-2118 93.63 %
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)
11.4833-0.07450.82281.43150.02821.7579-0.00130.1627-0.0614-0.18160.0028-0.08290.06240.1494-0.0014-0.1068-0.00770.0301-0.1073-0.0021-0.125414.733311.106910.1473
20.67570.64720.1752.65530.94821.51110.0093-0.060.04570.0867-0.02530.0807-0.0132-0.0190.016-0.14750.00160.0084-0.10590.0018-0.122316.584122.145428.6893
315.877415.54484.342520.14731.95452.2585-0.1060.09480.340.01180.13250.32080.01390.0353-0.0264-0.11940.0019-0.004-0.1222-0.0122-0.14112.206520.585717.5483
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 991 - 99
22BB1 - 991 - 99
33AD301

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