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- PDB-1dif: HIV-1 PROTEASE IN COMPLEX WITH A DIFLUOROKETONE CONTAINING INHIBI... -

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Basic information

Entry
Database: PDB / ID: 1dif
TitleHIV-1 PROTEASE IN COMPLEX WITH A DIFLUOROKETONE CONTAINING INHIBITOR A79285
ComponentsHIV-1 PROTEASE
KeywordsASPARTIC PROTEINASE
Function / homology
Function and homology information


induction by virus of host cysteine-type endopeptidase activity involved in apoptotic process / ec:3.4.23.16: / ec:3.1.26.13: / ec:3.1.13.2: / exoribonuclease H activity / host multivesicular body / viral penetration into host nucleus / ec:2.7.7.49: / DNA integration / viral genome integration into host DNA ...induction by virus of host cysteine-type endopeptidase activity involved in apoptotic process / ec:3.4.23.16: / ec:3.1.26.13: / ec:3.1.13.2: / exoribonuclease H activity / host multivesicular body / viral penetration into host nucleus / ec:2.7.7.49: / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase activity / ec:2.7.7.-: / establishment of integrated proviral latency / suppression by virus of host gene expression / RNA-DNA hybrid ribonuclease activity / viral entry into host cell / viral nucleocapsid / DNA recombination / lipid binding / ec:3.1.-.-: / ec:2.7.7.7: / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / DNA binding / zinc ion binding
Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, N-terminal / Immunodeficiency lentiviral matrix, N-terminal / Reverse transcriptase domain / Retroviral nucleocapsid protein Gag / Integrase, C-terminal, retroviral / Integrase, catalytic core / Zinc finger, CCHC-type / Aspartic peptidase, active site / Ribonuclease H domain ...Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, N-terminal / Immunodeficiency lentiviral matrix, N-terminal / Reverse transcriptase domain / Retroviral nucleocapsid protein Gag / Integrase, C-terminal, retroviral / Integrase, catalytic core / Zinc finger, CCHC-type / Aspartic peptidase, active site / Ribonuclease H domain / Integrase, N-terminal zinc-binding domain / Retrovirus capsid, C-terminal / Reverse transcriptase connection / RNase H / Reverse transcriptase thumb / Retroviral matrix protein / Ribonuclease H-like superfamily / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Integrase-like, N-terminal / Retropepsins / Aspartic peptidase domain superfamily / Retropepsin-like catalytic domain / Ribonuclease H superfamily / Integrase, C-terminal domain superfamily, retroviral / Retroviral aspartyl protease / Zinc finger, CCHC-type superfamily / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase connection domain / Integrase DNA binding domain profile. / Integrase catalytic domain profile. / RNase H domain profile. / Reverse transcriptase (RT) catalytic domain profile. / Zinc finger integrase-type profile. / Aspartyl protease, retroviral-type family profile. / Zinc finger CCHC-type profile. / Zinc knuckle / Reverse transcriptase thumb domain / Eukaryotic and viral aspartyl proteases active site. / Integrase Zinc binding domain / Integrase core domain / gag gene protein p24 (core nucleocapsid protein) / Integrase DNA binding domain / gag gene protein p17 (matrix protein)
Gag-Pol polyprotein
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsSilva, A.M. / Cachau, R.E. / Sham, H.L. / Erickson, J.W.
CitationJournal: J.Mol.Biol. / Year: 1996
Title: Inhibition and catalytic mechanism of HIV-1 aspartic protease.
Authors: Silva, A.M. / Cachau, R.E. / Sham, H.L. / Erickson, J.W.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 9, 1995 / Release: Mar 8, 1996
RevisionDateData content typeGroupProviderType
1.0Mar 8, 1996Structure modelrepositoryInitial release
1.1Mar 3, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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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)22,5955
Polymers21,6082
Non-polymers9873
Water2,828157
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-37 kcal/mol
Surface area9330 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)52.000, 59.900, 62.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide HIV-1 PROTEASE / / HIV-1 PR


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 / Production host: Escherichia coli (E. coli) / References: UniProt: P03367
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / 2-Mercaptoethanol
#3: Chemical ChemComp-A85 / N-{1-BENZYL-2,2-DIFLUORO-3,3-DIHYDROXY-4-[3-METHYL-2-(3-METHYL-3-PYRIDIN-2-YLMETHYL-UREIDO)-BUTYRYLAMINO]-5-PHENYL-PENTYL}-3-METHYL-2-(3-METHYL-3-PYRIDIN-2-YLMETHYL-UREIDO)-BUTYRAMIDE


Mass: 830.962 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H56F2N8O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal grow
*PLUS
pH: 6.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS

Crystal-ID: 1

IDConc.Common nameSol-ID
18 mg/mlproteasedrop
250 mMsodium acetatedrop
310 mMdithiothreitoldrop
437 %(w/v)ammonium sulfatereservoir
563 mMcitratereservoir
6126 mMsodium phosphatereservoir
71 Mbeta-mercaptoethanolreservoir
8dimethyl sulfoxidereservoir
9isopropanolreservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 20479 / % possible obs: 94.9 % / Redundancy: 2 % / Rmerge(I) obs: 0.0094
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. measured all: 40709 / Rmerge(I) obs: 0.092

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
X-PLORphasing
RefinementResolution: 1.7→10 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.198 -
Obs0.198 17589
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3126 0 134 471 3731
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Type: x_dihedral_angle_deg / Dev ideal: 29.1

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