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- PDB-2upj: HIV-1 PROTEASE COMPLEX WITH U100313 ([3-[[3-[CYCLOPROPYL [4-HYDRO... -

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Basic information

Entry
Database: PDB / ID: 2upj
TitleHIV-1 PROTEASE COMPLEX WITH U100313 ([3-[[3-[CYCLOPROPYL [4-HYDROXY-2OXO-6-[1-(PHENYLMETHYL)PROPYL]-2H-PYRAN-3-YL] METHYL]PHENYL]AMINO]-3-OXO-PROPYL]CARBAMIC ACID TERT-BUTYL ESTER)
ComponentsHIV-1 PROTEASE
KeywordsHYDROLASE (ACID PROTEASE)
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / host multivesicular body / viral penetration into host nucleus / 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 / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / 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 / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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-U02 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWatenpaugh, K.D. / Mulichak, A.M. / Janakiraman, M.N.
CitationJournal: J.Med.Chem. / Year: 1995
Title: Structure-based design of novel HIV protease inhibitors: carboxamide-containing 4-hydroxycoumarins and 4-hydroxy-2-pyrones as potent nonpeptidic inhibitors.
Authors: Thaisrivongs, S. / Watenpaugh, K.D. / Howe, W.J. / Tomich, P.K. / Dolak, L.A. / Chong, K.-T. / Tomich, C.-S.C. / Tomasselli, A.G. / Turner, S.R. / Strohbach, J.W. / Mulichak, A.M. / ...Authors: Thaisrivongs, S. / Watenpaugh, K.D. / Howe, W.J. / Tomich, P.K. / Dolak, L.A. / Chong, K.-T. / Tomich, C.-S.C. / Tomasselli, A.G. / Turner, S.R. / Strohbach, J.W. / Mulichak, A.M. / Janakiraman, M.N. / Moon, J.B. / Lynn, J.C. / Horng, M.-M. / Hinshaw, R.R. / Curry, K.A. / Rothrock, D.J.
History
DepositionMar 4, 1996Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 22, 2012Group: Database references
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 PROTEASE
B: HIV-1 PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1663
Polymers21,6082
Non-polymers5591
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-34 kcal/mol
Surface area9380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.260, 87.214, 46.192
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


Mass: 10803.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: BH5 / Production host: Escherichia coli (E. coli) / References: UniProt: P03367, HIV-1 retropepsin
#2: Chemical ChemComp-U02 / [2-(3-{[6-(1-BENZYL-PROPYL)-4-HYDROXY-2-OXO-2H-PYRAN-3-YL]-CYCLOPROPYL-METHYL}-PHENYLCARBAMOYL)-ETHYL]-CARBAMIC ACID TERT-BUTYL ESTER


Mass: 558.665 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H38N2O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE INHIBITOR MOLECULE BINDS IN ONE ONE ORIENTATION. HOWEVER, THE CARBOXAMIDE SIDE CHAIN WITH ITS ...THE INHIBITOR MOLECULE BINDS IN ONE ONE ORIENTATION. HOWEVER, THE CARBOXAMIDE SIDE CHAIN WITH ITS BOC GROUP COULD HAVE AN ALTERNATE CONFORMATION IN THE SAME DIRECTION. REGARDING RESIDUE *PCP* OF THE INHIBITOR: ATOMS OA2 AND OA3 ARE, RESPECTIVELY, THE CARBONYL OXYGEN AND RING OXYGEN OF THE LACTONIC FUNCTION. THE ATOM OA6 IS THE HYDROXYLIC OXYGEN OF THE PYRONE TEMPLATE.

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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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growpH: 5.2 / Details: pH 5.2
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.75-2.0 M1reservoirNaCl
20.1 Macetate1reservoir

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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: Nov 5, 1993
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→10 Å / Num. obs: 5144 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 6
Reflection shellResolution: 3→3.2 Å / Redundancy: 5 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3.8 / % possible all: 100
Reflection
*PLUS
Num. measured all: 30558

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Processing

Software
NameClassification
MERLOTphasing
CEDARrefinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EARLIER STRUCTURE

Resolution: 3→10 Å / σ(F): 2
Details: NO ELECTRON DENSITY WAS OBSERVED BEYOND THE POSITION OF THE BETA-CARBON FOR GLU A 34, ARG A 41, GLN A 61, AND GLN B 18, THE DELTA-CARBON OF LYS A 14, LYS A 43, AND LYS B 55. THEY WERE ...Details: NO ELECTRON DENSITY WAS OBSERVED BEYOND THE POSITION OF THE BETA-CARBON FOR GLU A 34, ARG A 41, GLN A 61, AND GLN B 18, THE DELTA-CARBON OF LYS A 14, LYS A 43, AND LYS B 55. THEY WERE PRESENT DURING REFINEMENT, HOWEVER. IN ADDITION, ATOMS WITH B-FACTORS GREATER THAN 70.0 A**2 MAY BE CONSIDERED TO BE DISORDERED OR NOT SEEN IN THE ELECTRON DENSITY MAPS.
RfactorNum. reflection
Rwork0.144 -
obs-4333
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 41 56 1613
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.011
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.866
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Software
*PLUS
Name: CEDAR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.164
Solvent computation
*PLUS
Displacement parameters
*PLUS

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