4B3Q 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: Exoribonuclease H, P66 Rt, Reverse Transcriptase P Subunit;
Ec: 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2, 3.4.23.16
Engineered: Yes
Mutation: Yes
Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676
Expression_system: Escherichia Coli
Expression_system_taxid: 1007065
Expression_system_strain: M15
Expression_system_vector_type: Plasmid
Expression_system_vector: Pdmi.1

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

Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676
Expression_system: Escherichia Coli
Expression_system_taxid: 1007065
Expression_system_strain: M15
Expression_system_vector_type: Plasmid
Expression_system_vector: Pdmi.1

Molecule: Primer Dna
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Template Rna
Chain: R
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: H 3 2
R_factor 0.361 R_Free 0.407
crystal
cell
length a length b length c angle alpha angle beta angle gamma
272.700 272.700 233.100 90.00 90.00 120.00
method X-Ray Diffractionresolution 5.00 Å
ligand NVP 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] (177 Kb) [Save to disk]
  • Biological Unit Coordinates (4b3q.pdb1.gz) 169 Kb
  • LPC: Ligand-Protein Contacts for 4B3Q
  • CSU: Contacts of Structural Units for 4B3Q
  • Structure Factors (73 Kb)
  • Retrieve 4B3Q in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4B3Q from S2C, [Save to disk]
  • Re-refined 4b3q structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4B3Q 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 4B3Q
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4B3Q, from MSDmotif at EBI
  • Fold representative 4b3q from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4b3q_D] [4b3q_A] [4b3q] [4b3q_B] [4b3q_R]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4B3Q
  • Community annotation for 4B3Q at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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