4B3O Hydrolase Dna Rna date Jul 25, 2012
title Structures Of Hiv-1 Rt And Rna-Dna Complex Reveal A Unique R Conformation And Substrate Interface
authors M.Lapkouski, L.Tian, J.T.Miller, S.F.J.Le Grice, W.Yang
compound source
Molecule: Reverse Transcriptaseribonuclease H
Chain: A
Synonym: Reverse Transcriptase, Exoribonuclease H, P66 Rt, Transcriptase P66 Subunit;
Ec: 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.4.23.16, 3.1.13.2
Engineered: Yes
Mutation: Yes
Organism_scientific: Human Immunodeficiency Virus 1
Organism_common: Hiv-1
Organism_taxid: 11676
Expression_system: Escherichia Coli
Expression_system_taxid: 1007065
Expression_system_strain: M15pdmi.1
Expression_system_vector_type: Plasmid

Molecule: P51 Rt
Chain: B
Synonym: Reverse Transcriptase, Reverse Transcriptase P51 S
Ec: 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.4.23.16
Engineered: Yes
Mutation: Yes

Organism_scientific: Human Immunodeficiency Virus 1
Organism_common: Hiv-1
Organism_taxid: 11676
Expression_system: Escherichia Coli
Expression_system_taxid: 1007065
Expression_system_strain: M15pdmi.1
Expression_system_vector_type: Plasmid

Molecule: 5'-D(Cpgptpaptpgpcpcptpaptpapgptp Tpaptptpgptpgpgpcpc)-3';
Chain: D
Synonym: Primer Dna
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-R(Apupgpap3drpgpgpcpcpapcpapapup Apcpupapupapgpgpcpapupa)-3';
Chain: R
Synonym: Template Rna
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 31 2 1
R_factor 0.275 R_Free 0.295
crystal
cell
length a length b length c angle alpha angle beta angle gamma
164.598 164.598 129.030 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.30 Å
ligand 3DR, CA, EFZ BindingDB enzyme Transferase E.C.2.7.7.49 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceComplexes of HIV-1 RT, NNRTI and RNA/DNA hybrid reveal a structure compatible with RNA degradation., Lapkouski M, Tian L, Miller JT, Le Grice SF, Yang W, Nat Struct Mol Biol. 2013 Jan 13. doi: 10.1038/nsmb.2485. PMID:23314251
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (182 Kb) [Save to disk]
  • Biological Unit Coordinates (4b3o.pdb1.gz) 173 Kb
  • LPC: Ligand-Protein Contacts for 4B3O
  • CSU: Contacts of Structural Units for 4B3O
  • Structure Factors (607 Kb)
  • Retrieve 4B3O in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4B3O from S2C, [Save to disk]
  • Re-refined 4b3o structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4B3O 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 4B3O
  • 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 4B3O, from MSDmotif at EBI
  • Fold representative 4b3o from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4b3o_B] [4b3o_R] [4b3o_D] [4b3o_A] [4b3o]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4B3O
  • Community annotation for 4B3O at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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