5J2Q Transferase Dna date Mar 29, 2016
title Hiv-1 Reverse Transcriptase In Complex With Dna That Has Inc A Mismatched Efda-Mp At The N-(Pre-Translocation) Site
authors Z.L.Salie, K.A.Kirby, S.G.Sarafianos
compound source
Molecule: Hiv-1 Reverse Transcriptase P66 Subunit
Chain: A
Synonym: Pr160gag-Pol
Ec: 2.7.7.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Human Immunodeficiency Virus Type 1 Gr Subtype B (Isolate Hxb2);
Organism_common: Hiv-1
Organism_taxid: 11706
Strain: Isolate Hxb2
Gene: Gag-Pol
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)-Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcdfduet1

Molecule: Hiv-1 Reverse Transcriptase P51 Domain
Chain: B
Synonym: Pr160gag-Pol
Ec: 2.7.7.-
Engineered: Yes
Mutation: Yes

Organism_scientific: Human Immunodeficiency Virus Type 1 Gr Subtype B (Isolate Hxb2);
Organism_common: Hiv-1
Organism_taxid: 11706
Strain: Isolate Hxb2
Gene: Gag-Pol
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)-Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prsfduet1

Molecule: Dna (5'- D(Apcpapgptpcpcpcptpgptptpcpgpgp(Mrg) Pcpgpcpcp(6fm)P(6fm))-3');
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676

Molecule: Dna (27-Mer)
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676
symmetry Space Group: C 2 2 21
R_factor 0.212 R_Free 0.252
crystal
cell
length a length b length c angle alpha angle beta angle gamma
165.557 170.512 102.235 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.79 Å
ligand 6FM, MG, MRG enzyme Transferase E.C.2.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceStructural basis of HIV inhibition by translocation-defective RT inhibitor 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA)., Salie ZL, Kirby KA, Michailidis E, Marchand B, Singh K, Rohan LC, Kodama EN, Mitsuya H, Parniak MA, Sarafianos SG, Proc Natl Acad Sci U S A. 2016 Aug 16;113(33):9274-9. doi:, 10.1073/pnas.1605223113. Epub 2016 Aug 3. PMID:27489345
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (372 Kb) [Save to disk]
  • Biological Unit Coordinates (5j2q.pdb1.gz) 365 Kb
  • LPC: Ligand-Protein Contacts for 5J2Q
  • CSU: Contacts of Structural Units for 5J2Q
  • Structure Factors (438 Kb)
  • Retrieve 5J2Q in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5J2Q from S2C, [Save to disk]
  • Re-refined 5j2q structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5J2Q 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 5J2Q
  • 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
  • Fold representative 5j2q from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5j2q_B] [5j2q_P] [5j2q] [5j2q_A] [5j2q_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5J2Q
  • Community annotation for 5J2Q at PDBWiki (http://pdbwiki.org)

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