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- PDB-1upj: HIV-1 PROTEASE COMPLEX WITH U095438 [3-[1-(4-BROMOPHENYL) ISOBUTY... -

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Basic information

Entry
Database: PDB / ID: 1upj
TitleHIV-1 PROTEASE COMPLEX WITH U095438 [3-[1-(4-BROMOPHENYL) ISOBUTYL]-4-HYDROXYCOUMARIN
ComponentsHIV-1 PROTEASE
KeywordsHYDROLASE (ACID PROTEASE)
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-U01 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 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.C. / Tomasselli, A.G. / Turner, S.R. / Strohbach, J.W. / Mulichak, A.M. / Janakiraman, ...Authors: Thaisrivongs, S. / Watenpaugh, K.D. / Howe, W.J. / Tomich, P.K. / Dolak, L.A. / Chong, K.T. / Tomich, C.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. / Rothroc, D.J.
History
DepositionMar 4, 1996Processing site: BNL
Revision 1.0Oct 14, 1996Provider: 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 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / 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

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Assembly

Deposited unit
A: HIV-1 PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1772
Polymers10,8041
Non-polymers3731
Water1,67593
1
A: HIV-1 PROTEASE
hetero molecules

A: HIV-1 PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3544
Polymers21,6082
Non-polymers7462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Unit cell
Length a, b, c (Å)63.475, 63.475, 84.100
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-53-

PHE

21A-201-

U01

31A-358-

HOH

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Components

#1: Protein HIV-1 PROTEASE


Mass: 10803.756 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-U01 / 3-[1-(4-BROMO-PHENYL)-2-METHYL-PROPYL]-4-HYDROXY-CHROMEN-2-ONE / PARA-BROMOPHENYL ANALOGUE OF PHEN-PROCOUMON 3-(ALPHA-ETHYLBENZYL)-4-HYDROXYCOUMARIN


Mass: 373.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17BrO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsREGARDING RESIDUE U01 [THE INHIBITOR]: THE ATOMS OA2 AND OA3 ARE, RESPECTIVELY, THE CARBONYL OXYGEN ...REGARDING RESIDUE U01 [THE INHIBITOR]: THE 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 COUMARIN 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: 2.26 Å3/Da / Density % sol: 45.63 %
Crystal growpH: 5.4 / Details: pH 5.4
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 Mcitrate1reservoir

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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: Jan 6, 1992
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.22→10 Å / Num. obs: 4806 / % possible obs: 89.5 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 10.2
Reflection shellResolution: 2.22→2.36 Å / Redundancy: 3 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 1.8 / % possible all: 46
Reflection
*PLUS
Num. measured all: 31369
Reflection shell
*PLUS
% possible obs: 46 %

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Processing

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

Resolution: 2.22→10 Å / σ(F): 2
Details: AS ONLY ONE MOLECULE OF THE INHIBITOR CAN INHIBIT THE DIMERIC PROTEASE BY BINDING TO ITS ACTIVE SITE, THE ATOMS BELONGING TO THE INHIBITOR MOLECULE ARE [TO BE] GIVEN AN OCCUPANCY FACTOR OF 0. ...Details: AS ONLY ONE MOLECULE OF THE INHIBITOR CAN INHIBIT THE DIMERIC PROTEASE BY BINDING TO ITS ACTIVE SITE, THE ATOMS BELONGING TO THE INHIBITOR MOLECULE ARE [TO BE] GIVEN AN OCCUPANCY FACTOR OF 0.5 EACH IN THE SPACE GROUP P6(1)22. NO ALTERNATE CONFORMATIONS ARE OBSERVED FOR THE INHIBITOR. NO ELECTRON DENSITY WAS OBSERVED BEYOND THE POSITION OF THE BETA-CARBON FOR GLU 34, ARG 41, PHE 53, AND GLN 61, THE DELTA-CARBON OF LYS 45, AND LYS 55, AND THE EPSILON-CARBON OF RESIDUE ARG 57. 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. SIDE CHAIN ATOMS OF THE THE PHENYL GROUP OF RESIDUE PHE 53 HAVE BEEN MODELED IN ONLY ONE OF THE TWO ALTERNATE CONFORMATIONS AND ASSIGNED AN OCCUPANCY OF 0.5. NO ATOMS IN THE FORM OF DUMMY WATER MOLECULES ARE INTRODUCED AT THE SITE CORRESPONDING TO THE ALTERNATE CONFORMATION. SEE REMARK 6 ALSO. THE BROMINE ATOM OF THE INHIBITOR WAS TREATED AS "S" WITH AN OCCUPANCY OF UNITY DURING CRYSTALLOGRAPHIC REFINEMENTS.
RfactorNum. reflection
Rwork0.193 -
obs-3957
Refinement stepCycle: LAST / Resolution: 2.22→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms758 0 23 93 874
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.012
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_deg3.056
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: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS

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