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- PDB-2won: Crystal Structure of UK-453061 bound to HIV-1 Reverse Transcripta... -

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Basic information

Entry
Database: PDB / ID: 2won
TitleCrystal Structure of UK-453061 bound to HIV-1 Reverse Transcriptase (wild-type).
Components(HIV-1 REVERSE TRANSCRIPTASEReverse transcriptase) x 2
KeywordsTRANSFERASE / AIDS / NON-NUCLEOSIDE INHIBITOR / DRUG DESIGN / NNRTI / SBDD
Function / homology
Function and homology information


integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / : / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / protein processing / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / peptidase activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding
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. / 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 / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain 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-ZZE / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.8 Å
AuthorsPhillips, C. / Irving, S.L. / Knoechel, T. / Ringrose, H.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2010
Title: Lersivirine: A Non-Nucleoside Reverse Transcriptase Inhibitor with Activity Against Drug- Resistant Human Immunodeficiency Virus-1.
Authors: Corbau, R. / Mori, J. / Phillips, C. / Fishburn, L. / Martin, A. / Mowbray, C. / Panton, W. / Smith-Burchnell, C. / Thornberry, A. / Ringrose, H. / Knoechel, T. / Irving, S.L. / Westby, M. / ...Authors: Corbau, R. / Mori, J. / Phillips, C. / Fishburn, L. / Martin, A. / Mowbray, C. / Panton, W. / Smith-Burchnell, C. / Thornberry, A. / Ringrose, H. / Knoechel, T. / Irving, S.L. / Westby, M. / Wood, A. / Perros, M.
History
DepositionJul 27, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 REVERSE TRANSCRIPTASE
B: HIV-1 REVERSE TRANSCRIPTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,2723
Polymers115,9622
Non-polymers3101
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-28.2 kcal/mol
Surface area45330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.490, 154.250, 154.880
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 HIV-1 REVERSE TRANSCRIPTASE / Reverse transcriptase / HIV-1 RT


Mass: 64562.949 Da / Num. of mol.: 1 / Fragment: P66, RESIDUES 588-1147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P04585, RNA-directed DNA polymerase
#2: Protein HIV-1 REVERSE TRANSCRIPTASE / Reverse transcriptase / HIV-1 RT


Mass: 51399.047 Da / Num. of mol.: 1 / Fragment: P51, RESIDUES 588-1027
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P04585, RNA-directed DNA polymerase
#3: Chemical ChemComp-ZZE / 5-{[3,5-diethyl-1-(2-hydroxyethyl)-1H-pyrazol-4-yl]oxy}benzene-1,3-dicarbonitrile


Mass: 310.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18N4O2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.35 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. obs: 32451 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 73.58 Å2 / Rmerge(I) obs: 0.04

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Processing

SoftwareName: BUSTER-TNT / Version: 2.9.2 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.8→24.88 Å / Cor.coef. Fo:Fc: 0.9055 / Cor.coef. Fo:Fc free: 0.8833 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1629 5.02 %RANDOM
Rwork0.253 ---
obs-32427 99.1 %-
Displacement parametersBiso mean: 63.12 Å2
Baniso -1Baniso -2Baniso -3
1-4.5576 Å20 Å20 Å2
2--7.0149 Å20 Å2
3----11.5725 Å2
Refine analyzeLuzzati coordinate error obs: 0.529 Å
Refinement stepCycle: LAST / Resolution: 2.8→24.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7921 0 23 0 7944
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0078155HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9611079HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2846SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes227HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1110HARMONIC5
X-RAY DIFFRACTIONt_it8155HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.09
X-RAY DIFFRACTIONt_other_torsion18.1
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1054SEMIHARMONIC5
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_contact9602SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.89 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.3517 135 4.5 %
Rwork0.3202 2864 -

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