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- PDB-5ivr: Crystal Structure of HIV Protease complexed with methyl N-[(1S)-1... -

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Basic information

Entry
Database: PDB / ID: 5ivr
TitleCrystal Structure of HIV Protease complexed with methyl N-[(1S)-1-[[2-[(3S)-3-[(4-aminophenyl)methylamino]-4-hydroxy-butyl]phenyl]carbamoyl]-2,2-diphenyl-ethyl]carbamate
ComponentsProtease
KeywordsHYDROLASE/INHIBITOR / HIV / protease / HYDROLASE-INHIBITOR complex
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 / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsSu, H.P.
CitationJournal: Acs Med.Chem.Lett. / Year: 2016
Title: Discovery of MK-8718, an HIV Protease Inhibitor Containing a Novel Morpholine Aspartate Binding Group.
Authors: Bungard, C.J. / Williams, P.D. / Ballard, J.E. / Bennett, D.J. / Beaulieu, C. / Bahnck-Teets, C. / Carroll, S.S. / Chang, R.K. / Dubost, D.C. / Fay, J.F. / Diamond, T.L. / Greshock, T.J. / ...Authors: Bungard, C.J. / Williams, P.D. / Ballard, J.E. / Bennett, D.J. / Beaulieu, C. / Bahnck-Teets, C. / Carroll, S.S. / Chang, R.K. / Dubost, D.C. / Fay, J.F. / Diamond, T.L. / Greshock, T.J. / Hao, L. / Holloway, M.K. / Felock, P.J. / Gesell, J.J. / Su, H.P. / Manikowski, J.J. / McKay, D.J. / Miller, M. / Min, X. / Molinaro, C. / Moradei, O.M. / Nantermet, P.G. / Nadeau, C. / Sanchez, R.I. / Satyanarayana, T. / Shipe, W.D. / Singh, S.K. / Truong, V.L. / Vijayasaradhi, S. / Wiscount, C.M. / Vacca, J.P. / Crane, S.N. / McCauley, J.A.
History
DepositionMar 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3707
Polymers21,6622
Non-polymers7095
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-62 kcal/mol
Surface area9720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.190, 85.960, 46.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Protease


Mass: 10830.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli) / References: UniProt: Q77VV3
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-6EG / N-{2-[(3S)-3-{[(4-aminophenyl)methyl]amino}-4-hydroxybutyl]phenyl}-Nalpha-(methoxycarbonyl)-beta-phenyl-L-phenylalaninamide


Mass: 566.690 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H38N4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.68 Å3/Da / Density % sol: 54.03 % / Mosaicity: 0.09 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: NaCl / PH range: 5.0-5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Nov 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→48.19 Å / Num. obs: 35192 / % possible obs: 91.6 % / Redundancy: 4.6 % / Biso Wilson estimate: 17.37 Å2 / CC1/2: 0.968 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.09 / Rrim(I) all: 0.211 / Net I/σ(I): 6.7 / Num. measured all: 163487
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.591.70.246561932120.8830.20.3192.452.8
4.49-48.195.20.193802815460.9540.0910.2148.699.1

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Processing

Software
NameVersionClassification
Aimless0.3.6data scaling
BUSTER2.11.5refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→48.19 Å / Cor.coef. Fo:Fc: 0.9393 / Cor.coef. Fo:Fc free: 0.9263 / SU R Cruickshank DPI: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.078 / SU Rfree Blow DPI: 0.074 / SU Rfree Cruickshank DPI: 0.071
RfactorNum. reflection% reflectionSelection details
Rfree0.2067 1748 4.98 %RANDOM
Rwork0.1926 ---
obs0.1933 35086 92.34 %-
Displacement parametersBiso max: 83.81 Å2 / Biso mean: 18.84 Å2 / Biso min: 8.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.8202 Å20 Å20 Å2
2--1.0259 Å20 Å2
3----0.2057 Å2
Refine analyzeLuzzati coordinate error obs: 0.167 Å
Refinement stepCycle: final / Resolution: 1.5→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1520 0 46 197 1763
Biso mean--26.03 29.17 -
Num. residues----198
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d569SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes40HARMONIC8
X-RAY DIFFRACTIONt_gen_planes238HARMONIC8
X-RAY DIFFRACTIONt_it1604HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion218SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1969SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1604HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2176HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion3.08
X-RAY DIFFRACTIONt_other_torsion14.11
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2584 61 4.73 %
Rwork0.2368 1228 -
all0.2378 1289 -
obs--92.34 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.56240.0230.20540.60550.40460.61150.01590.0569-0.0225-0.0526-0.0253-0.0150.03710.04040.00940.007-0.00160.01060.00510.0038-0.0054-14.380411.0088-12.9686
20.16820.28970.11411.08460.42140.823-0.0053-0.02730.01070.03930.0080.04640.0194-0.01-0.0027-0.01480.0030.00110.00060.00250.0056-12.796822.21735.7488
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 99
2X-RAY DIFFRACTION2{ B|* }B1 - 99

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