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

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Basic information

Entry
Database: PDB / ID: 2wom
TitleCrystal Structure of UK-453061 bound to HIV-1 Reverse Transcriptase (K103N).
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 / Early Phase of HIV Life Cycle / Vpr-mediated nuclear import of PICs / 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 / Early Phase of HIV Life Cycle / Vpr-mediated nuclear import of PICs / 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 / : / retroviral ribonuclease H / Budding and maturation of HIV virion / 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 / host cell plasma membrane / virion membrane / structural molecule activity / 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 / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsPhillips, C. / Irving, S.L. / Knoechel, T. / Ringrose, H.
CitationJournal: Antimicrob. Agents Chemother. / Year: 2010
Title: Lersivirine, a nonnucleoside reverse transcriptase inhibitor with activity against drug-resistant human immunodeficiency virus type 1.
Authors: Corbau, R. / Mori, J. / Phillips, C. / Fishburn, L. / Martin, A. / Mowbray, C. / Panton, W. / Smith-Burchnell, C. / Thornberry, A. / Ringrose, H. / Knochel, T. / Irving, S. / 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 1.1Jan 29, 2014Group: Version format compliance
Revision 1.2Jun 20, 2018Group: Data collection / Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / diffrn_source / refine
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type / _refine.pdbx_method_to_determine_struct / _refine.pdbx_starting_model
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)116,2423
Polymers115,9322
Non-polymers3101
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-28.2 kcal/mol
Surface area45300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.600, 154.300, 155.400
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: 64547.871 Da / Num. of mol.: 1 / Fragment: P66, RESIDUES 588-1147 / Mutation: YES
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: 51383.969 Da / Num. of mol.: 1 / Fragment: P51, RESIDUES 588-1027 / Mutation: YES
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
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 690 TO ASN ENGINEERED RESIDUE IN CHAIN B, LYS 690 TO ASN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.2 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→25 Å / Num. obs: 23100 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 72.63 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15

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Processing

SoftwareName: BUSTER-TNT / Version: 2.9.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1fkp

1fkp


Resolution: 3.2→24.95 Å / Cor.coef. Fo:Fc: 0.8905 / Cor.coef. Fo:Fc free: 0.8615 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2574 1184 5.13 %RANDOM
Rwork0.2277 ---
obs0.2291 23079 --
Displacement parametersBiso mean: 52.75 Å2
Baniso -1Baniso -2Baniso -3
1-2.4494 Å20 Å20 Å2
2--5.276 Å20 Å2
3----7.7254 Å2
Refine analyzeLuzzati coordinate error obs: 0.641 Å
Refinement stepCycle: LAST / Resolution: 3.2→24.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7919 0 23 0 7942
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0078152HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9811076HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2841SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes229HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1109HARMONIC5
X-RAY DIFFRACTIONt_it8152HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.21
X-RAY DIFFRACTIONt_other_torsion18.33
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_contact9495SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.34 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3047 137 4.94 %
Rwork0.2824 2636 -
all0.2836 2773 -

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