3JYT Transferase Dna Complex date Sep 22, 2009
title K65r Mutant Hiv-1 Reverse Transcriptase Cross-Linked To Ds-D Complexed With Datp As The Incoming Nucleotide Substrate
authors K.Das, E.Arnold
compound source
Molecule: Reverse Transcriptaseribonuclease H
Chain: A
Synonym: Exoribonuclease H,P66 Rt
Ec: 2.7.7.49
Engineered: Yes
Mutation: Yes
Organism_scientific: Human Immunodeficiency Virus Type 1 Gr Subtype B (Isolate Bh10);
Organism_common: Hiv-1
Organism_taxid: 11678
Strain: Isolate Bh10
Gene: Gag-Pol
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Dh5alpha

Molecule: P51 Rt
Chain: B
Engineered: Yes
Mutation: Yes

Organism_scientific: Human Immunodeficiency Virus Type 1 Gr Subtype B (Isolate Bh10);
Organism_common: Hiv-1
Organism_taxid: 11678
Strain: Isolate Bh10
Gene: Gag-Pol
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Dh5alpha

Molecule: Dna (5'- D(Atpgpgptpcpgpgpcpgpcpcpcpgpapapcpapgp Ptpgptpg)-3');
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Chemically Modified With Thiol-Dgmp And Enzy Terminated With Ddgtp;

Molecule: Dna (5'- D(Acpapgptpcpcpcptpgptptpcpgpgp(Mrg) Pcpgpcpcp(Ddg))-3');
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 31 1 2
R_factor 0.253 R_Free 0.287
crystal
cell
length a length b length c angle alpha angle beta angle gamma
169.720 169.720 155.410 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.30 Å
ligand DDG, DTP, MG, MRG, SO4 enzyme Transferase E.C.2.7.7.49 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceStructural basis for the role of the K65r mutation in HIV-1 reverse transcriptase polymerization, excision antagonism, and tenofovir resistance., Das K, Bandwar RP, White KL, Feng JY, Sarafianos SG, Tuske S, Tu X, Clark AD Jr, Boyer PL, Hou X, Gaffney BL, Jones RA, Miller MD, Hughes SH, Arnold E, J Biol Chem. 2009 Dec 11;284(50):35092-100. Epub 2009 Oct 7. PMID:19812032
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (185 Kb) [Save to disk]
  • Biological Unit Coordinates (3jyt.pdb1.gz) 176 Kb
  • LPC: Ligand-Protein Contacts for 3JYT
  • CSU: Contacts of Structural Units for 3JYT
  • Structure Factors (328 Kb)
  • Retrieve 3JYT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3JYT from S2C, [Save to disk]
  • Re-refined 3jyt structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3JYT in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3JYT
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3JYT, from MSDmotif at EBI
  • Fold representative 3jyt from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3jyt_P] [3jyt_A] [3jyt] [3jyt_T] [3jyt_B]
  • SWISS-PROT database: [P03366]
  • Domain organization of [POL_HV1B1] by SWISSPFAM
  • Other resources with information on 3JYT
  • Community annotation for 3JYT at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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