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- PDB-6prf: HIV-1 Protease multiple drug resistant clinical isolate mutant PR... -

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Basic information

Entry
Database: PDB / ID: 6prf
TitleHIV-1 Protease multiple drug resistant clinical isolate mutant PR20 with GRL-14213A
ComponentsProtease
KeywordsHydrolase/Hydrolase Inhibitor / Protease / Inhibitor / Multiple Mutant / Viral Protein complex / HYDROLASE / Hydrolase-Hydrolase Inhibitor / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


HIV-1 retropepsin / 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 ...HIV-1 retropepsin / 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 / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / 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. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / 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. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-7OA / YTTRIUM ION / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.21 Å
AuthorsKneller, D.W. / Agniswamy, J. / Weber, I.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AI150461 United States
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Potent antiviral HIV-1 protease inhibitor combats highly drug resistant mutant PR20.
Authors: Kneller, D.W. / Agniswamy, J. / Ghosh, A.K. / Weber, I.T.
History
DepositionJul 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,04012
Polymers21,5332
Non-polymers1,50710
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-80 kcal/mol
Surface area10170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.565, 60.565, 85.139
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 Protease / PR / Retropepsin


Mass: 10766.542 Da / Num. of mol.: 2
Mutation: Q7K, L10F, I13V, I15V, D30N, V32I, L33F, E35D, M36I, S37N, I47V, I54L, Q58E, I62V, L63P, C67A, A71V, I84V, N88D, L89T, L90M, C95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype
Strain: isolate PR20 / Gene: gag-pol / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P03366, HIV-1 retropepsin
#2: Chemical
ChemComp-Y1 / YTTRIUM ION


Mass: 88.906 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Y
#3: Chemical ChemComp-7OA / (3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl [(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3,5-difluorophenyl)-3-hydroxybutan-2-yl]carbamate


Mass: 706.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H40F2N4O7S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.05 Å3/Da / Density % sol: 40.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.8 M sodium chloride, 0.1 M sodium acetate pH 5.5, 0.01M yittrium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.21→50 Å / Num. obs: 46059 / % possible obs: 99.7 % / Redundancy: 7.5 % / Biso Wilson estimate: 21.518 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.033 / Rrim(I) all: 0.098 / Χ2: 0.985 / Net I/σ(I): 21
Reflection shellResolution: 1.21→1.25 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2 / Num. unique obs: 2127 / CC1/2: 0.676 / Rpim(I) all: 0.362 / Rrim(I) all: 0.623 / Χ2: 1.1 / % possible all: 90

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YHQ

4yhq


Resolution: 1.21→28.55 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.606 / SU ML: 0.032 / SU R Cruickshank DPI: 0.0587 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.055 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1897 2194 4.8 %RANDOM
Rwork0.1522 ---
obs0.154 43734 84.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 179.78 Å2 / Biso mean: 21.518 Å2 / Biso min: 9.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.02 Å2-0 Å2
2---0.03 Å20 Å2
3---0.11 Å2
Refinement stepCycle: final / Resolution: 1.21→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 105 226 1849
Biso mean--14.15 31.73 -
Num. residues----198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0122002
X-RAY DIFFRACTIONr_angle_refined_deg2.1791.6462786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2085270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51822.38184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98815338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.841510
X-RAY DIFFRACTIONr_chiral_restr0.1350.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021520
X-RAY DIFFRACTIONr_rigid_bond_restr17.46632002
LS refinement shellResolution: 1.21→1.239 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.281 61 -
Rwork0.315 1403 -
obs--36.55 %

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