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- PDB-5cop: X-ray crystal structure of wild type HIV-1 protease in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5cop
TitleX-ray crystal structure of wild type HIV-1 protease in complex with GRL-097
ComponentsHIV-1 protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / GRL-097 / HIV-1 protease / protease-inhibitor / darunavir / Tp-THF / nonpeptidic / hydroxyl / O-methoxy. / HYDROLASE-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
Chem-53F / Pol protein / Pol protein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsYedidi, R.S. / Hayashi, H. / Aoki, M. / Das, D. / Ghosh, A.K. / Mitsuya, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J.Virol. / Year: 2015
Title: C-5-Modified Tetrahydropyrano-Tetrahydofuran-Derived Protease Inhibitors (PIs) Exert Potent Inhibition of the Replication of HIV-1 Variants Highly Resistant to Various PIs, including Darunavir.
Authors: Aoki, M. / Hayashi, H. / Yedidi, R.S. / Martyr, C.D. / Takamatsu, Y. / Aoki-Ogata, H. / Nakamura, T. / Nakata, H. / Das, D. / Yamagata, Y. / Ghosh, A.K. / Mitsuya, H.
History
DepositionJul 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)22,2133
Polymers21,6062
Non-polymers6081
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-24 kcal/mol
Surface area9250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.663, 62.663, 81.955
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein HIV-1 protease


Mass: 10802.771 Da / Num. of mol.: 2 / Fragment: UNP residues 1-99
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: G0X8E3, UniProt: G0X8E8*PLUS
#2: Chemical ChemComp-53F / (3R,3aS,4S,7aS)-3-hydroxyhexahydro-4H-furo[2,3-b]pyran-4-yl [(2S,3R)-4-{[(4-aminophenyl)sulfonyl](2-methylpropyl)amino}-3-hydroxy-1-(4-methoxyphenyl)butan-2-yl]carbamate


Mass: 607.716 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H41N3O9S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium dihydrogen phosphate pH6.5, 12% (weight/volume) polyethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 12252 / % possible obs: 98.7 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 23.035
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 2.889 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4 Å32.71 Å
Translation4 Å32.71 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
MOLREP10.2.35phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→31.332 Å / FOM work R set: 0.7832 / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.92 / Phase error: 28.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2674 589 4.82 %
Rwork0.2022 11641 -
obs0.2052 12230 98.84 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.441 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 65.19 Å2 / Biso mean: 29.64 Å2 / Biso min: 10.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.1972 Å20 Å2-0 Å2
2--0.1972 Å20 Å2
3----0.3944 Å2
Refinement stepCycle: final / Resolution: 2→31.332 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 84 116 1716
Biso mean--24.2 34.34 -
Num. residues----198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091632
X-RAY DIFFRACTIONf_angle_d1.192218
X-RAY DIFFRACTIONf_chiral_restr0.079262
X-RAY DIFFRACTIONf_plane_restr0.005266
X-RAY DIFFRACTIONf_dihedral_angle_d16.483640
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0003-2.20160.3321590.241829023061100
2.2016-2.520.30421560.23022908306499
2.52-3.17450.2741430.21112904304799
3.1745-31.33530.23131310.17962927305898

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