3KK2 Transferase Dna date Nov 04, 2009
title Hiv-1 Reverse Transcriptase-Dna Complex With Datp Bound In T Nucleotide Binding Site
authors E.B.Lansdon
compound source
Molecule: Reverse Transcriptase P66 Subunit
Chain: A
Synonym: P66 Rt
Ec: 2.7.7.49
Engineered: Yes
Mutation: Yes
Organism_scientific: Human Immunodeficiency Virus Type 1
Organism_common: Hiv-1
Organism_taxid: 11706
Strain: Hxb2d
Gene: Gag-Pol
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet14b

Molecule: Reverse Transcriptase P51 Subunit
Chain: B
Synonym: P51 Rt
Ec: 2.7.7.49
Engineered: Yes
Mutation: Yes

Organism_scientific: Human Immunodeficiency Virus Type 1
Organism_common: Hiv-1
Organism_taxid: 11706
Strain: Hxb2d
Gene: Gag-Pol
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet14b

Molecule: 5'-D(Apcpagptpcpcpcptpgptptpcpgpgp Cpcp(Doc))-3';
Chain: P
Engineered: Yes
Other_details: Primer Dna

Synthetic: Yes

Molecule: 5'-D(Atpgpgptpgpgpgpcpgpcpcpcpgpap Gpgpgpapcptpgptpg)-3';
Chain: T
Engineered: Yes
Other_details: Template Dna

Synthetic: Yes
symmetry Space Group: C 2 2 21
R_factor 0.198 R_Free 0.259
crystal
cell
length a length b length c angle alpha angle beta angle gamma
167.912 168.922 102.041 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand DOC, DTP, MG, SO4 enzyme Transferase E.C.2.7.7.49 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceVisualizing the Molecular Interactions of a Nucleotide Analog, GS-9148, with HIV-1 Reverse Transcriptase-DNA Complex., Lansdon EB, Samuel D, Lagpacan L, Brendza KM, White KL, Hung M, Liu X, Boojamra CG, Mackman RL, Cihlar T, Ray AS, McGrath ME, Swaminathan S, J Mol Biol. 2010 Feb 13. PMID:20156454
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (187 Kb) [Save to disk]
  • Biological Unit Coordinates (3kk2.pdb1.gz) 177 Kb
  • LPC: Ligand-Protein Contacts for 3KK2
  • CSU: Contacts of Structural Units for 3KK2
  • Structure Factors (210 Kb)
  • Retrieve 3KK2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KK2 from S2C, [Save to disk]
  • Re-refined 3kk2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3KK2 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 3KK2
  • 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 3KK2, from MSDmotif at EBI
  • Fold representative 3kk2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3kk2] [3kk2_P] [3kk2_T] [3kk2_B] [3kk2_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3KK2
  • Community annotation for 3KK2 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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