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- PDB-4npt: Crystal Structure of HIV-1 Protease Multiple Mutant P51 Complexed... -

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Basic information

Entry
Database: PDB / ID: 4npt
TitleCrystal Structure of HIV-1 Protease Multiple Mutant P51 Complexed with Darunavir
ComponentsProtease
KeywordsHYDROLASE / HIV-1 protease / darunavir / P51 / multiple mutant / drug resistance
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 / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsZhang, Y. / Weber, I.T.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Structures of darunavir-resistant HIV-1 protease mutant reveal atypical binding of darunavir to wide open flaps.
Authors: Zhang, Y. / Chang, Y.C. / Louis, J.M. / Wang, Y.F. / Harrison, R.W. / Weber, I.T.
History
DepositionNov 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4253
Polymers10,7861
Non-polymers6402
Water86548
1
A: Protease
hetero molecules

A: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8516
Polymers21,5712
Non-polymers1,2804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area5600 Å2
ΔGint-31 kcal/mol
Surface area9900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.804, 46.804, 100.627
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-541-

HOH

21A-542-

HOH

31A-543-

HOH

41A-548-

HOH

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Components

#1: Protein Protease


Mass: 10785.679 Da / Num. of mol.: 1
Mutation: Q7K, D25N, V32I, L33F, N37S, V54M, C67A, Q70K, A82I, I84V, C95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O38896
#2: Chemical ChemComp-017 / (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE / Darunavir / TMC114 / UIC-94017


Mass: 547.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H37N3O7S / Comment: medication, antiretroviral*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.55 Å3/Da / Density % sol: 51.85 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES sodium, 0.8 M Potassium sodium tartrate tetrahydrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 29, 2012
RadiationMonochromator: SI220 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. all: 13867 / Num. obs: 13867 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 18.5
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 3.3 / % possible all: 98.3

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3UF3

3uf3


Resolution: 1.66→22.16 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.553 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22632 691 5 %RANDOM
Rwork0.18901 ---
all0.19077 13867 --
obs0.19077 13173 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.436 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.66→22.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms760 0 44 48 852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.019839
X-RAY DIFFRACTIONr_bond_other_d0.0010.02848
X-RAY DIFFRACTIONr_angle_refined_deg2.3262.0321144
X-RAY DIFFRACTIONr_angle_other_deg0.95231953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0525102
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.45824.13829
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31415144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.78155
X-RAY DIFFRACTIONr_chiral_restr0.1210.2135
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021911
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02178
LS refinement shellResolution: 1.66→1.701 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 51 -
Rwork0.229 918 -
obs--97.68 %
Refinement TLS params.Method: refined / Origin x: 4.8286 Å / Origin y: -3.092 Å / Origin z: 13.7058 Å
111213212223313233
T0.0521 Å20.0006 Å2-0.0029 Å2-0.0394 Å20.0101 Å2--0.0624 Å2
L0.2542 °2-0.1266 °2-0.2804 °2-0.1189 °20.0118 °2--1.1696 °2
S0.0303 Å °0.0085 Å °0.0162 Å °-0.0489 Å °-0.0206 Å °-0.0257 Å °0.0266 Å °-0.1058 Å °-0.0097 Å °

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