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- PDB-1zp8: HIV Protease with inhibitor AB-2 -

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Basic information

Entry
Database: PDB / ID: 1zp8
TitleHIV Protease with inhibitor AB-2
ComponentsPol polyprotein
KeywordsHYDROLASE / protease / retroviral
Function / homology
Function and homology information


HIV-1 retropepsin / 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 ...HIV-1 retropepsin / 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 / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / 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. / 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 / 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. / 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-AB2 / Protease / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / REFINEMENT / Resolution: 2.02 Å
AuthorsBrik, A. / Alexandratos, J.N. / Elder, J.H. / Olson, A.J. / Wlodawer, A. / Goodsell, D.S. / Wong, C.H.
CitationJournal: Chembiochem / Year: 2005
Title: 1,2,3-triazole as a peptide surrogate in the rapid synthesis of HIV-1 protease inhibitors.
Authors: Brik, A. / Alexandratos, J. / Lin, Y.C. / Elder, J.H. / Olson, A.J. / Wlodawer, A. / Goodsell, D.S. / Wong, C.H.
History
DepositionMay 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pol polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4692
Polymers10,8051
Non-polymers6641
Water1,44180
1
A: Pol polyprotein
hetero molecules

A: Pol polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9374
Polymers21,6102
Non-polymers1,3282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+2/31
Buried area6130 Å2
ΔGint-12 kcal/mol
Surface area9330 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.100, 63.100, 82.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-200-

AB2

21A-301-

HOH

31A-369-

HOH

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Components

#1: Protein Pol polyprotein


Mass: 10804.808 Da / Num. of mol.: 1 / Fragment: HIV Protease
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-PLysS
References: UniProt: P03368, UniProt: O92139*PLUS, HIV-1 retropepsin
#2: Chemical ChemComp-AB2 / [1-((1S,2R)-1-BENZYL-2-HYDROXY-3-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}PROPYL)-1H-1,2,3-TRIAZOL-4-YL]METHYL (1R,2R)-2-HYDROXY-2,3-DIHYDRO-1H-INDEN-1-YLCARBAMATE


Mass: 663.784 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H41N5O7S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.2 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.34 M Ammonium Sulfate, 0.1 M Na Acetate, pH 4.8-5.4, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0089 / Wavelength: 1.0089 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 7, 2003
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0089 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. all: 6185 / Num. obs: 5931 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Rsym value: 0.054 / Net I/σ(I): 34.4
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.94 / Rsym value: 0.352 / % possible all: 67

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Processing

Software
NameVersionClassificationNB
SHELXrefinement
PDB_EXTRACT1.6data extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: REFINEMENT
Starting model: PDB entry 3TLH

3tlh


Resolution: 2.02→10 Å / Num. parameters: 3579 / Num. restraintsaints: 3317 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.326 484 8.2 %RANDOM
Rwork0.197 ---
all0.196 5931 --
obs0.197 5931 85.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 30.742 Å2
Refinement stepCycle: LAST / Resolution: 2.02→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms758 0 47 80 885
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.0420
X-RAY DIFFRACTIONs_similar_dist00
X-RAY DIFFRACTIONs_from_restr_planes0.0210
X-RAY DIFFRACTIONs_zero_chiral_vol0.0260
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.0330
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.0120
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt00
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.090
X-RAY DIFFRACTIONs_approx_iso_adps00
LS refinement shellResolution: 2.02→2.09 Å

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