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- PDB-1hih: COMPARATIVE ANALYSIS OF THE X-RAY STRUCTURES OF HIV-1 AND HIV-2 P... -

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Basic information

Entry
Database: PDB / ID: 1hih
TitleCOMPARATIVE ANALYSIS OF THE X-RAY STRUCTURES OF HIV-1 AND HIV-2 PROTEASES IN COMPLEX WITH CGP 53820, A NOVEL PSEUDOSYMMETRIC INHIBITOR
ComponentsHIV-1 PROTEASE
KeywordsHYDROLASE (ASPARTIC PROTEINASE) / ASPARTATE PROTEASE / INHIBITED / HIV
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 / 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. / 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 / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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
BETA-MERCAPTOETHANOL / Chem-C20 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsPriestle, J.P. / Gruetter, M.G.
Citation
Journal: Structure / Year: 1995
Title: Comparative analysis of the X-ray structures of HIV-1 and HIV-2 proteases in complex with CGP 53820, a novel pseudosymmetric inhibitor.
Authors: Priestle, J.P. / Fassler, A. / Rosel, J. / Tintelnot-Blomley, M. / Strop, P. / Grutter, M.G.
#1: Journal: Bioorg.Med.Chem.Lett. / Year: 1993
Title: Novel Pseudosymmetric Inhibitors of HIV-1 Protease
Authors: Fassler, A. / Rosel, J. / Tintelnot-Blomley, M. / Alteri, E. / Bold, G. / Lang, M.
History
DepositionMar 31, 1995Processing site: BNL
Revision 1.0Jul 10, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site

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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)22,3385
Polymers21,6082
Non-polymers7303
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-30 kcal/mol
Surface area9180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.000, 59.300, 61.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9989, -0.04432, -0.015), (-0.00121, -0.29604, 0.95517), (-0.04678, 0.95415, 0.29567)
Vector: 10.34, -15.65, 11.96)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 1 .. A 99 B 1 .. B 99 0.677

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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 / Cell line: S2 / Gene: POL / Plasmid: PT7Q10H / Gene (production host): POL / Production host: Escherichia coli (E. coli)
References: UniProt: P03366, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-C20 / ACETYL-NH-VAL-CYCLOHEXYL-CH2[NCH2CHOH]CH2-BENZYL-VAL-NH-ACETYL / CGP 53820


Mass: 573.767 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H51N5O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCOMPND MOLECULE: HIV-1 PROTEASE. BRU ISOLATE.
Nonpolymer detailsSOURCE 1 MOLECULE_NAME: CGP 53820. PSEUDOSYMMETRIC TRANSITION-STATE ANALOG. SOURCE 2 MOLECULE_NAME: ...SOURCE 1 MOLECULE_NAME: CGP 53820. PSEUDOSYMMETRIC TRANSITION-STATE ANALOG. SOURCE 2 MOLECULE_NAME: BETA-MERCAPTOETHANOL (BME). PSEUDOSYMMETRIC TRANSITION-STATE ANALOG.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal
*PLUS
Density % sol: 45 %
Crystal grow
*PLUS
pH: 5.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 mg/mlenzyme1drop
210 mg/mldimethylsulfoxide1drop
315-30 %satammonium sulfate1drop
40.1 Msodium acetate1reservoir
515-30 %satammonium sulfate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Aug 1, 1993
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 10082 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.05 % / Rmerge(I) obs: 0.057
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. measured all: 30789 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.26 Å / Rmerge(I) obs: 0.226

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
MADNESdata reduction
X-PLORphasing
RefinementResolution: 2.2→6 Å / σ(F): 0 /
RfactorNum. reflection% reflection
obs0.144 9515 99 %
Displacement parametersBiso mean: 23.8 Å2
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 49 145 1710
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg1.83
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_improper_angle_d
X-RAY DIFFRACTIONt_improper_angle_deg1.42

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