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- PDB-5fdl: Crystal Structure of K103N/Y181C Mutant HIV-1 Reverse Transcripta... -

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Basic information

Entry
Database: PDB / ID: 5fdl
TitleCrystal Structure of K103N/Y181C Mutant HIV-1 Reverse Transcriptase (RT) in Complex with IDX899
Components
  • P51 Reverse transcriptase
  • P66 Reverse transcriptase
KeywordsHYDROLASE / HIV-1 Reverse Transcriptase / Phosphoindole / NNRTI / Mutation
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / 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. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-5DV / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Human immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsDousson, C.B. / Alexandre, F.-R. / Convard, T. / Fisher, M. / Lamers, M.B.A.C. / Leonard, P.M.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Discovery of the Aryl-phospho-indole IDX899, a Highly Potent Anti-HIV Non-nucleoside Reverse Transcriptase Inhibitor.
Authors: Dousson, C. / Alexandre, F.R. / Amador, A. / Bonaric, S. / Bot, S. / Caillet, C. / Convard, T. / da Costa, D. / Lioure, M.P. / Roland, A. / Rosinovsky, E. / Maldonado, S. / Parsy, C. / ...Authors: Dousson, C. / Alexandre, F.R. / Amador, A. / Bonaric, S. / Bot, S. / Caillet, C. / Convard, T. / da Costa, D. / Lioure, M.P. / Roland, A. / Rosinovsky, E. / Maldonado, S. / Parsy, C. / Trochet, C. / Storer, R. / Stewart, A. / Wang, J. / Mayes, B.A. / Musiu, C. / Poddesu, B. / Vargiu, L. / Liuzzi, M. / Moussa, A. / Jakubik, J. / Hubbard, L. / Seifer, M. / Standring, D.
History
DepositionDec 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: P51 Reverse transcriptase
B: P66 Reverse transcriptase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,7983
Polymers115,3822
Non-polymers4161
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-31 kcal/mol
Surface area43470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.260, 154.790, 154.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein P51 Reverse transcriptase / Pr160Gag-Pol


Mass: 64086.426 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: P51 / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag-pol / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P03366, RNA-directed DNA polymerase
#2: Protein P66 Reverse transcriptase / Pr160Gag-Pol


Mass: 51295.926 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: P66 / Source: (gene. exp.) Human immunodeficiency virus type 1 / Gene: gag-pol / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P03366, RNA-directed DNA polymerase
#3: Chemical ChemComp-5DV / methyl (R)-(2-carbamoyl-5-chloro-1H-indol-3-yl)[3-(2-cyanoethyl)-5-methylphenyl]phosphinate


Mass: 415.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19ClN3O3P

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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: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein was concentrated to 14 mg/ml in the presence of 0.5 mM inhibitor A051606P then used in successive crystal micro-seeding experiments to yield protein crystals of 0.3 mm x 0.3 mm x 0.2 ...Details: Protein was concentrated to 14 mg/ml in the presence of 0.5 mM inhibitor A051606P then used in successive crystal micro-seeding experiments to yield protein crystals of 0.3 mm x 0.3 mm x 0.2 mm in 1.4 M Sodium Malonate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.1→94.15 Å / Num. obs: 26048 / % possible obs: 99.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 6.6
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.831 / Mean I/σ(I) obs: 1.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Aimlessdata scaling
PHASERphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KO0

4ko0


Resolution: 3.1→94.15 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.845 / SU B: 30.378 / SU ML: 0.495 / Cross valid method: THROUGHOUT / ESU R Free: 0.517 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29866 1255 4.8 %RANDOM
Rwork0.24279 ---
obs0.24549 24765 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.782 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å2-0 Å20 Å2
2---1.13 Å2-0 Å2
3---2.33 Å2
Refinement stepCycle: LAST / Resolution: 3.1→94.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7425 0 28 0 7453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.027656
X-RAY DIFFRACTIONr_bond_other_d0.0010.027166
X-RAY DIFFRACTIONr_angle_refined_deg1.0941.95510463
X-RAY DIFFRACTIONr_angle_other_deg0.837316517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4895940
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01725.492315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4151247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8151518
X-RAY DIFFRACTIONr_chiral_restr0.060.21169
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218677
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021641
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1356.7373778
X-RAY DIFFRACTIONr_mcbond_other2.1356.7373779
X-RAY DIFFRACTIONr_mcangle_it3.80210.0984712
X-RAY DIFFRACTIONr_mcangle_other3.80210.0984713
X-RAY DIFFRACTIONr_scbond_it1.5746.6993878
X-RAY DIFFRACTIONr_scbond_other1.5736.6993879
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.92210.0245751
X-RAY DIFFRACTIONr_long_range_B_refined5.62952.8818389
X-RAY DIFFRACTIONr_long_range_B_other5.6352.888386
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 93 -
Rwork0.347 1805 -
obs--100 %

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