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- PDB-1mtr: HIV-1 PROTEASE COMPLEXED WITH A CYCLIC PHE-ILE-VAL PEPTIDOMIMETIC... -

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Basic information

Entry
Database: PDB / ID: 1mtr
TitleHIV-1 PROTEASE COMPLEXED WITH A CYCLIC PHE-ILE-VAL PEPTIDOMIMETIC INHIBITOR
ComponentsHIV-1 PROTEASE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ASPARTYL PROTEINASE / AIDS / ASPARTYL PROTEASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / 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
tert-butyl [(1S,2S)-1-benzyl-2-hydroxy-3-{[(8S,11R)-8-[(1R)-1-methylpropyl]-7,10-dioxo-2-oxa-6,9-diazabicyclo[11.2.2]heptadeca-1(15),13,16-trien-11-yl]amino}propyl]carbamate / Chem-PI6 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 1.75 Å
AuthorsWickramasinghe, W. / Begun, J. / Martin, J.L.
CitationJournal: J.Am.Chem.Soc. / Year: 1996
Title: Substrate-based cyclic peptidomimetics of Phe-Ile-Val that inhibit HIV-1 protease using a novel enzyme-binding mode.
Authors: March, D.R. / Abbenante, G. / Bergman, D.A. / Brinkworth, R.I. / Wickramasinghe, W. / Begun, J. / Martin, J.L. / Fairlie, D.P.
History
DepositionFeb 15, 1996Processing site: BNL
Revision 1.0Aug 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Aug 24, 2011Group: Non-polymer description
Revision 1.4Jul 25, 2012Group: Non-polymer description
Revision 1.5Sep 19, 2012Group: Non-polymer description
Revision 1.6Dec 12, 2012Group: Other
Revision 1.7Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.8Aug 9, 2023Group: 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
B: HIV-1 PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4166
Polymers21,5312
Non-polymers8854
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-58 kcal/mol
Surface area9020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.400, 58.700, 62.000
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 HIV-1 PROTEASE


Mass: 10765.687 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: P03369, HIV-1 retropepsin
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PI6 / [1-BENZYL-3-(8-SEC-BUTYL-7,10-DIOXO-2-OXA-6,9-DIAZA-BICYCLO[11.2.2] HEPTADECA-1(16),13(17),14-TRIEN-11-YLAMINO)-2-HYDROXY-PROPYL]-CARBAMIC ACID TERT-BUTYL ESTER / MACROCYCLIC PEPTIDOMIMETIC INHIBITOR 6


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 596.757 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H48N4O6
References: tert-butyl [(1S,2S)-1-benzyl-2-hydroxy-3-{[(8S,11R)-8-[(1R)-1-methylpropyl]-7,10-dioxo-2-oxa-6,9-diazabicyclo[11.2.2]heptadeca-1(15),13,16-trien-11-yl]amino}propyl]carbamate
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGLN 7 WAS REPLACED BY LYS TO PREVENT AUTOCLEAVAGE. LEU 33 WAS REPLACED BY ILE TO PREVENT ...GLN 7 WAS REPLACED BY LYS TO PREVENT AUTOCLEAVAGE. LEU 33 WAS REPLACED BY ILE TO PREVENT AUTOCLEAVAGE. CYS 67 WAS REPLACED BY ABA FOR EASE OF CHEMICAL SYNTHESIS. CYS 95 WAS REPLACED BY ABA FOR EASE OF CHEMICAL SYNTHESIS.

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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: 2.11 Å3/Da / Density % sol: 44 %
Crystal growpH: 5.5 / Details: pH 5.5
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
145 %1reservoir(NH4)2SO4
20.1 Macetate1reservoir

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 28, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 16528 / % possible obs: 85.9 % / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.5
Reflection shellResolution: 1.75→2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 2.42 / % possible all: 69.2

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
PROCESS(HIGASHI/RIGAKU)data reduction
PROCESSdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: 1CPI

1cpi


Resolution: 1.75→8 Å / σ(F): 2
Details: RESIDUES 50 AND 51 IN THE FLAP REGION OF BOTH SUBUNITS ARE DISORDERED AND WERE MODELLED IN TWO CONFORMATIONS. HOWEVER, THESE REGIONS OF THE STRUCTURE HAVE RELATIVELY POOR GEOMETRY.
RfactorNum. reflection% reflection
Rfree0.244 1661 10 %
Rwork0.179 --
obs0.179 16283 84 %
Displacement parametersBiso mean: 18.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.75→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1500 0 58 115 1673
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.66
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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