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- PDB-1hpo: HIV-1 PROTEASE TRIPLE MUTANT/U103265 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1hpo
TitleHIV-1 PROTEASE TRIPLE MUTANT/U103265 COMPLEX
ComponentsHIV-1 PROTEASE
KeywordsHYDROLASE / ACID PROTEASE / ASPARTYL PROTEASE
Function / homology
Function and homology information


telomerase activity / 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 ...telomerase activity / 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 / 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 / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / viral translational frameshifting / 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-UNI / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWatenpaugh, K.D. / Janakiraman, M.N.
Citation
Journal: J.Med.Chem. / Year: 1997
Title: Structure-based design of nonpeptidic HIV protease inhibitors: the sulfonamide-substituted cyclooctylpyramones.
Authors: Skulnick, H.I. / Johnson, P.D. / Aristoff, P.A. / Morris, J.K. / Lovasz, K.D. / Howe, W.J. / Watenpaugh, K.D. / Janakiraman, M.N. / Anderson, D.J. / Reischer, R.J. / Schwartz, T.M. / Banitt, ...Authors: Skulnick, H.I. / Johnson, P.D. / Aristoff, P.A. / Morris, J.K. / Lovasz, K.D. / Howe, W.J. / Watenpaugh, K.D. / Janakiraman, M.N. / Anderson, D.J. / Reischer, R.J. / Schwartz, T.M. / Banitt, L.S. / Tomich, P.K. / Lynn, J.C. / Horng, M.M. / Chong, K.T. / Hinshaw, R.R. / Dolak, L.A. / Seest, E.P. / Schwende, F.J. / Rush, B.D. / Howard, G.M. / Toth, L.N. / Wilkinson, K.R. / Kakuk, T.J. / Johnson, C.W. / Cole, S.L. / Zaya, R.M. / Zipp, G.L. / Possert, P.L. / Dalga, R.J. / Zhong, W.-Z. / Williams, M.G. / Romines, K.R.
#1: Journal: J.Med.Chem. / Year: 1995
Title: Structure-based design of sulfonamide-substituted non-peptidic HIV protease inhibitors.
Authors: Skulnick, H.I. / Johnson, P.D. / Howe, W.J. / Tomich, P.K. / Chong, K.T. / Watenpaugh, K.D. / Janakiraman, M.N. / Dolak, L.A. / McGrath, J.P. / Lynn, J.C. / Horng, M.-M. / Hinshaw, R.B. / ...Authors: Skulnick, H.I. / Johnson, P.D. / Howe, W.J. / Tomich, P.K. / Chong, K.T. / Watenpaugh, K.D. / Janakiraman, M.N. / Dolak, L.A. / McGrath, J.P. / Lynn, J.C. / Horng, M.-M. / Hinshaw, R.B. / Zipp, G.L. / Ruwart, M.J. / Schwende, F.J. / Padbury, G.E. / Dalga, R.J. / Zhong, W.-Z. / Shiou, L. / Possert, P.L. / Rush, Bob D. / Wilkinson, Karen F. / Howard, Gina M. / Toth, L.N. / Williams, M.G. / Kakuk, T.J. / Cole, S.L. / Zaya, R.M. / Lovasz, K.D. / Morris, J.K. / Romines, K.R. / Thaisrivongs, S. / Aristoff, P.A.
History
DepositionDec 10, 1996Processing site: BNL
Revision 1.0Apr 21, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 22, 2012Group: Database references
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Nov 3, 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 1.6Feb 7, 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: HIV-1 PROTEASE
B: HIV-1 PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1143
Polymers21,6102
Non-polymers5051
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-33 kcal/mol
Surface area9240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.543, 88.416, 46.484
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 HIV-1 PROTEASE / HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 PROTEASE


Mass: 10804.808 Da / Num. of mol.: 2 / Mutation: Q7K, L33I, L63I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P03367, HIV-1 retropepsin
#2: Chemical ChemComp-UNI / 4-CYANO-N-(3-CYCLOPROPYL(5,6,7,8,9,10-HEXAHYDRO-4-HYDROXY-2-OXO-CYCLOOCTA[B]PYRAN-3-YL)METHYL)PHENYL BENZENSULFONAMIDE


Mass: 504.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H28N2O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.4
Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE IN 10 UL HANGING DROPS OF EQUAL VOLUMES OF PROTEIN/INHIBITOR COMPLEX AND THE PRECIPITANT OF 0.75, 1.0 1.5 2.0 M NACL AT PH'S 4.8, 5.0 AND 5.2 (0.1 M ...Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE IN 10 UL HANGING DROPS OF EQUAL VOLUMES OF PROTEIN/INHIBITOR COMPLEX AND THE PRECIPITANT OF 0.75, 1.0 1.5 2.0 M NACL AT PH'S 4.8, 5.0 AND 5.2 (0.1 M ACETATE BUFFER) AND AT PH'S 5.4, 5.6 AND 5.8 (0.1 M CITRATE BUFFER)., vapor diffusion - hanging drop
PH range: 4.8-5.4, 5.0-5.6, 5.2-5.8
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 mg/mlinhibitor1drop
26 mg/mlprotease1drop
30.1 Macetate1reservoirprecipitant
40.1 Mcitrate1reservoirprecipitant
5sodium chloride1reservoirprecipitant
6precipitant1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Feb 28, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. obs: 9119 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 8.2
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 2.2 / % possible all: 92.5
Reflection
*PLUS
Num. measured all: 63195

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Processing

Software
NameClassification
MERLOTphasing
CEDARrefinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.179 --
obs-7560 82.9 %
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1491 0 36 164 1691
Software
*PLUS
Name: CEDAR / Classification: refinement
Refinement
*PLUS
Num. reflection all: 9119 / Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_deg2.618

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