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- PDB-1d4h: HIV-1 Protease in complex with the inhibitor BEA435 -

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Basic information

Entry
Database: PDB / ID: 1d4h
TitleHIV-1 Protease in complex with the inhibitor BEA435
ComponentsHIV-1 PROTEASE
KeywordsHYDROLASE / DIMER
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-BEH / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.81 Å
AuthorsUnge, T.
CitationJournal: Eur.J.Biochem. / Year: 2003
Title: Optimization of P1-P3 groups in symmetric and asymmetric HIV-1 protease inhibitors.
Authors: Andersson, H.O. / Fridborg, K. / Lowgren, S. / Alterman, M. / Muhlman, A. / Bjorsne, M. / Garg, N. / Kvarnstrom, I. / Schaal, W. / Classon, B. / Danielsson, U.H. / Ahlsen, G. / Nillroth, U. ...Authors: Andersson, H.O. / Fridborg, K. / Lowgren, S. / Alterman, M. / Muhlman, A. / Bjorsne, M. / Garg, N. / Kvarnstrom, I. / Schaal, W. / Classon, B. / Danielsson, U.H. / Ahlsen, G. / Nillroth, U. / Vrang, L. / Oberg, B. / Samuelsson, B. / Hallberg, A. / Unge, T.
History
DepositionOct 4, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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)22,2183
Polymers21,6082
Non-polymers6111
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-36 kcal/mol
Surface area9360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.457, 86.307, 46.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a dimer.

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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 / Genus: Lentivirus / Strain: BH10 / Plasmid: PET11C / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, HIV-1 retropepsin
#2: Chemical ChemComp-BEH / 2,5-DIBENZYLOXY-3,4-DIHYDROXY-HEXANEDIOIC ACID BENZYLAMIDE (2-HYDROXY-INDAN-1-YL)-AMIDE / INHIBITOR BEA435


Mass: 610.696 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H38N2O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: sodium chloride, MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5 / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.0 mg/mlprotein1drop
250 mMMES1droppH6.5
310 mMdithiothreitol1drop
41 mMEDTA1drop
550 mMMES1reservoirpH5.5
60.5 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.375
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 16, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.375 Å / Relative weight: 1
ReflectionResolution: 1.81→22.6 Å / Num. all: 22136 / Num. obs: 20047 / % possible obs: 90.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 10.7
Reflection shellResolution: 1.81→1.92 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.212 / Num. unique all: 2589 / % possible all: 75
Reflection
*PLUS
Num. measured all: 61625 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
Lowest resolution: 1.87 Å

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementResolution: 1.81→22.58 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1228777.99 / Data cutoff high rms absF: 1228777.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber / Details: Refined with CNS program system
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1015 5.1 %RANDOM
Rwork0.195 ---
all-22136 --
obs-20047 90.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.89 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso mean: 21.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.5 Å20 Å20 Å2
2---4.72 Å20 Å2
3---0.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.81→22.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 45 129 1690
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it0.731.5
X-RAY DIFFRACTIONc_mcangle_it1.272
X-RAY DIFFRACTIONc_scbond_it8.232
X-RAY DIFFRACTIONc_scangle_it3.862.5
LS refinement shellResolution: 1.81→1.92 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.235 129 4.7 %
Rwork0.212 2589 -
obs--75 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMBEA435.TOP
X-RAY DIFFRACTION3BEA435.PAR
Refinement
*PLUS
Lowest resolution: 22.6 Å / Rfactor Rfree: 0.234 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

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