3V81 Transferase Dna date Dec 22, 2011
title Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) With D Nonnucleoside Inhibitor Nevirapine
authors K.Das, S.E.Martinez, E.Arnold
compound source
Molecule: Hiv-1 Reverse Transcriptase P66 Subunit
Chain: A, C
Fragment: Unp Residues 600-1153
Ec: 2.7.7.49, 2.7.7.7
Engineered: Yes
Mutation: Yes
Organism_scientific: Human Immunodeficiency Virus Type 1 Bh
Organism_common: Hiv-1
Organism_taxid: 11678
Strain: Bh10 Isolate
Gene: Gag-Pol
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid

Molecule: Hiv-1 Reverse Transcriptase P51 Subunit
Chain: B, D
Fragment: Unp Residues 600-1027
Ec: 2.7.7.49, 2.7.7.7
Engineered: Yes

Organism_scientific: Human Immunodeficiency Virus Type 1 Bh
Organism_common: Hiv-1
Organism_taxid: 11678
Strain: Bh10 Isolate
Gene: Gag-Pol
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid

Molecule: Dna (5'- D(Aptpgpgpapapgpgpcpgpcpcpcpgpapapcpapgp Cptpgptpg)-3');
Chain: T, E
Engineered: Yes

Synthetic: Yes
Other_details: Synthesized

Molecule: Dna (5'- D(Acpapgptpcpcpcptpgptptpcpgpgp(Mrg) Pcpgpcpcp(Atm))-3');
Chain: P, F
Engineered: Yes

Synthetic: Yes
Other_details: Synthesized
symmetry Space Group: P 1 21 1
R_factor 0.251 R_Free 0.298
crystal
cell
length a length b length c angle alpha angle beta angle gamma
89.822 132.052 142.732 90.00 100.84 90.00
method X-Ray Diffractionresolution 2.85 Å
ligand ATM, MRG, NVP BindingDB enzyme Transferase E.C.2.7.7.49 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceHIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism., Das K, Martinez SE, Bauman JD, Arnold E, Nat Struct Mol Biol. 2012 Jan 22;19(2):253-9. doi: 10.1038/nsmb.2223. PMID:22266819
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (364 Kb) [Save to disk]
  • Biological Unit Coordinates (3v81.pdb1.gz) 181 Kb
  • Biological Unit Coordinates (3v81.pdb2.gz) 182 Kb
  • LPC: Ligand-Protein Contacts for 3V81
  • CSU: Contacts of Structural Units for 3V81
  • Structure Factors (616 Kb)
  • Retrieve 3V81 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3V81 from S2C, [Save to disk]
  • Re-refined 3v81 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3V81 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 3V81
  • 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 3V81, from MSDmotif at EBI
  • Fold representative 3v81 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3v81_B] [3v81_A] [3v81_F] [3v81_E] [3v81_P] [3v81] [3v81_T] [3v81_D] [3v81_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3V81
  • Community annotation for 3V81 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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