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- PDB-1mui: Crystal structure of HIV-1 protease complexed with Lopinavir. -

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Basic information

Entry
Database: PDB / ID: 1mui
TitleCrystal structure of HIV-1 protease complexed with Lopinavir.
Componentsprotease
KeywordsHYDROLASE
Function / homology
Function and homology information


aspartic-type endopeptidase activity / 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
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsStoll, V. / Qin, W. / Stewart, K.D. / Jakob, C. / Park, C. / Walter, K. / Simmer, R.L. / Helfrich, R. / Bussiere, D. / Kao, J. ...Stoll, V. / Qin, W. / Stewart, K.D. / Jakob, C. / Park, C. / Walter, K. / Simmer, R.L. / Helfrich, R. / Bussiere, D. / Kao, J. / Kempf, D. / Sham, H.L. / Norbeck, D.W.
CitationJournal: BIOORG.MED.CHEM. / Year: 2002
Title: X-ray Crystallographic Structure of ABT-378 (Lopinavir) Bound to HIV-1 Protease
Authors: Stoll, V. / Qin, W. / Stewart, K.D. / Jakob, C. / Park, C. / Walter, K. / Simmer, R.L. / Helfrich, R. / Bussiere, D. / Kao, J. / Kempf, D. / Sham, H.L. / Norbeck, D.W.
History
DepositionSep 23, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: protease
A: protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2363
Polymers21,6082
Non-polymers6291
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-27 kcal/mol
Surface area9520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.264, 63.264, 83.621
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein protease


Mass: 10803.756 Da / Num. of mol.: 2 / Fragment: residues 57-155 / Mutation: N37S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / References: UniProt: Q903J0, HIV-1 retropepsin
#2: Chemical ChemComp-AB1 / N-{1-BENZYL-4-[2-(2,6-DIMETHYL-PHENOXY)-ACETYLAMINO]-3-HYDROXY-5-PHENYL-PENTYL}-3-METHYL-2-(2-OXO-TETRAHYDRO-PYRIMIDIN-1-YL)-BUTYRAMIDE / ABT-378 / LOPINAVIR


Mass: 628.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H48N4O5 / Comment: antiretroviral, protease inhibitor*YM

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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: 2.23 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 295 K / pH: 4.6
Details: 100mM Na acetate, 0.4-0.8M NaCl, pH 4.6, temperature 295K
Crystal grow
*PLUS
Method: unknown
Details: Fizgerald, P.M.D., (1990) J. Biol. Chem., 265, 14209.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→33.24 Å / Num. obs: 4652 / % possible obs: 93.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: -2.1 Å2 / Rsym value: 0.096 / Net I/σ(I): 9.2
Reflection shellResolution: 2.8→2.9 Å / Rsym value: 0.345 / % possible all: 97.5

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNXrefinement
HKL-2000data reduction
CNXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb code 9HVP

9hvp


Resolution: 2.8→33 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.329 326 -Random
Rwork0.261 ---
obs0.309 4403 7.4 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.48 Å2-1.98 Å20 Å2
2--0.48 Å20 Å2
3----0.96 Å2
Refine analyzeLuzzati coordinate error obs: 0.5 Å / Luzzati sigma a obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.8→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 92 0 1608
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.93
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.048
RfactorNum. reflection% reflection
Rfree0.322 45 -
Rwork0.276 --
obs-634 86.7 %
Refinement
*PLUS
Lowest resolution: 33 Å / % reflection Rfree: 7 % / Rfactor obs: 0.309 / Rfactor Rfree: 0.32 / Rfactor Rwork: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Rfactor Rfree: 0.322 / Rfactor Rwork: 0.276

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