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- PDB-1d4l: HIV-1 PROTEASE COMPLEXED WITH A MACROCYCLIC PEPTIDOMIMETIC INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 1d4l
TitleHIV-1 PROTEASE COMPLEXED WITH A MACROCYCLIC PEPTIDOMIMETIC INHIBITOR
ComponentsHIV-1 PROTEASE
KeywordsHYDROLASE / HIV / PROTEASE / INHIBITOR / ANTIVIRAL
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 / symbiont-mediated suppression of host gene expression / 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 / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / 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. / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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. / 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
Chem-PI9 / Gag-Pol polyprotein
Similarity search - Component
MethodX-RAY DIFFRACTION / Resolution: 1.75 Å
AuthorsTyndall, J.D. / Reid, R.C. / Tyssen, D.P. / Jardine, D.K. / Todd, B. / Passmore, M. / March, D.R. / Pattenden, L.K. / Alewood, D. / Hu, S.H. ...Tyndall, J.D. / Reid, R.C. / Tyssen, D.P. / Jardine, D.K. / Todd, B. / Passmore, M. / March, D.R. / Pattenden, L.K. / Alewood, D. / Hu, S.H. / Alewood, P.F. / Birch, C.J. / Martin, J.L. / Fairlie, D.P.
Citation
Journal: J.Med.Chem. / Year: 2000
Title: Synthesis, stability, antiviral activity, and protease-bound structures of substrate-mimicking constrained macrocyclic inhibitors of HIV-1 protease.
Authors: Tyndall, J.D. / Reid, R.C. / Tyssen, D.P. / Jardine, D.K. / Todd, B. / Passmore, M. / March, D.R. / Pattenden, L.K. / Bergman, D.A. / Alewood, D. / Hu, S.H. / Alewood, P.F. / Birch, C.J. / ...Authors: Tyndall, J.D. / Reid, R.C. / Tyssen, D.P. / Jardine, D.K. / Todd, B. / Passmore, M. / March, D.R. / Pattenden, L.K. / Bergman, D.A. / Alewood, D. / Hu, S.H. / Alewood, P.F. / Birch, C.J. / Martin, J.L. / Fairlie, D.P.
#1: Journal: Biochemistry / Year: 1999
Title: Molecular Recognition of Macrocyclic Peptidomimetic Inhibitors by HIV-1 Protease.
Authors: Martin, J.L. / Begun, J. / Schindeler, A. / Wickramasinghe, W.A. / Alewood, D. / Alewood, P.F. / Bergman, D.A. / Brinkworth, R.I. / Abbenante, G. / March, D. / Reid, R.C. / Fairlie, D.P.
#2: Journal: 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. / Abbenante, G. / Bergman, D. / Brinkworth, R.I. / Wickramasinghe, W. / Begun, J. / Martin, J.L. / Fairlie, D.P.
#3: Journal: J.Am.Chem.Soc. / Year: 1995
Title: Regioselective Structural and Functional Mimicry Of Peptides: Design Of Hydrolytically Stable Cyclic Peptidomimetic Inhibitors Of HIV-1 Protease.
Authors: Abbenante, G. / March, D. / Bergman, D. / Hunt, P.A. / Garnham, B. / Dancer, R.J. / Martin, J.L. / Fairlie, D.P.
History
DepositionOct 4, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)22,4366
Polymers21,5312
Non-polymers9054
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-58 kcal/mol
Surface area9000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.440, 58.770, 61.710
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 / Mutation: Q7K, L33I, C67(ABA), C95(ABA) / Source method: obtained synthetically
Details: SF2 isolate, chemically synthesised protein corresponds to the protease from HIV-1, with 4 mutations per monomer
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-PI9 / (10S,13S,1'R)-13-[1'-HYDROXY-2'-(N-P-AMINOBENZENESULFONYL-1''-AMINO-3''-METHYLBUTYL)ETHYL]-8,11-DIOXO-10-ISOPROPYL-2-OXA-9,12-DIAZABICYCLO [13.2.2]NONADECA-15,17,18-TRIENE


Mass: 616.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H48N4O6S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.16 Å3/Da / Density % sol: 43.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: ammonium sulfate. acetate buffer, , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / Details: inhibitor:protein molar ratio is 10:1
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
30.1 Macetate1reservoir
435-60 %satammonium sulfate1reservoir
2inhibitor1dropin DMSO

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 8, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 62454 / Num. obs: 59019 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.38 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 9.5
Reflection shellResolution: 1.75→1.83 Å / Redundancy: 3.35 % / Rmerge(I) obs: 0.302 / Num. unique all: 1621 / % possible all: 84.6
Reflection
*PLUS
Num. obs: 18470 / Num. measured all: 62454
Reflection shell
*PLUS
% possible obs: 84.6 % / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 1.75→8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1791 9.8 %RANDOM
Rwork0.189 ---
all0.189 18244 --
obs0.189 18244 94.9 %-
Displacement parametersBiso mean: 19.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.75→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1540 0 60 121 1721
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.42
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.431.5
X-RAY DIFFRACTIONx_mcangle_it2.242
X-RAY DIFFRACTIONx_scbond_it2.512
X-RAY DIFFRACTIONx_scangle_it4.172.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 251 9.3 %
Rwork0.281 2459 -
obs--86.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1parhcsdx.protophcsdx.pro
X-RAY DIFFRACTION2nal.parInhibiter1.top
X-RAY DIFFRACTION3toph19.sol
X-RAY DIFFRACTION4so4.inp
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.42
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.32 / % reflection Rfree: 9.3 % / Rfactor Rwork: 0.281 / Rfactor obs: 0.288

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