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- PDB-2cen: P1' Extended HIV-1 Protease Inhibitors Encompassing a Tertiary Al... -

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Basic information

Entry
Database: PDB / ID: 2cen
TitleP1' Extended HIV-1 Protease Inhibitors Encompassing a Tertiary Alcohol in the Transition-State Mimicking Scaffold
ComponentsPOL PROTEIN
KeywordsHYDROLASE / HIV-1 / PROTEASE / INHIBITOR / ASPARTYL PROTEASE
Function / homology
Function and homology information


host multivesicular body / aspartic-type endopeptidase activity / virion membrane / proteolysis
Similarity search - Function
Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-4AH / Protease / Pol protein
Similarity search - Component
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGinman, N. / Ekegren, J.K. / Johansson, A. / Wallberg, H. / Larhed, M. / Samuelsson, B. / Hallberg, A. / Unge, T.
CitationJournal: J.Med.Chem. / Year: 2006
Title: Microwave-Accelerated Synthesis of P1'-Extended HIV-1 Protease Inhibitors Encompassing a Tertiary Alcohol in the Transition-State Mimicking Scaffold.
Authors: Ekegren, J.K. / Ginman, N. / Johansson, A. / Wallberg, H. / Larhed, M. / Samuelsson, B. / Unge, T. / Hallberg, A.
History
DepositionFeb 8, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" AND "BA" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" AND "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 7-STRANDED BARRELS REPRESENTED BY AN 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: POL PROTEIN
B: POL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2873
Polymers21,6082
Non-polymers6801
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.350, 85.750, 46.580
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 POL PROTEIN / HIV-1 PROTEASE


Mass: 10803.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: COMPLEX WITH INHIBITOR AHA478 / Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Strain: HIV-1 D10 / Variant: D10 / Plasmid: PET11D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA
References: UniProt: Q8Q3H0, UniProt: Q5RZ09*PLUS, HIV-1 retropepsin
#2: Chemical ChemComp-4AH / {(1S)-1-[N'-[(2S)-2-HYDROXY-2-((1S,2R)-2-HYDROXY-INDAN-1-YLCARBAMOYL)-3-PHENYL-PROPYL]-N'-[4-(PYRIDINE-2-YL)-BENZYL]-HYDRAZINOCARBONYL]-2,2-DIMETHYL-PROPYL}-CARBAMIC ACID METHYL ESTER


Mass: 679.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H45N5O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.75 Å3/Da / Density % sol: 54.97 %
Crystal growpH: 5
Details: 0.7 M NACL, 50 MM MESHCL, 14 MM BME, PH5.0, pH 5.00

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.7→48.2 Å / Num. obs: 26399 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.2
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EBW

1ebw


Resolution: 1.7→25 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 1316 5 %RANDOM
Rwork0.2207 ---
obs0.2207 26399 100 %-
Solvent computationBsol: 40.7437 Å2 / ksol: 0.379795 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.825 Å20 Å20 Å2
2--0.857 Å20 Å2
3----0.032 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 50 166 1732
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005959
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.37884
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PAR1205MOD.TXTTOP1205MOD.TXT
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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