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 Diffraction	resolution	3.30 Å
ligand	DDG, DTP, MG, MRG, SO4	enzyme	Transferase E.C.2.7.7.49 BRENDA
Gene Ontology	Chain Function Process Component A B
Primary reference	Structural 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] (183 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

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 3D motif for 3JYT, from MSDmotif at EBI

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)

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