1T05

HIV-1 reverse transcriptase crosslinked to template-primer with tenofovir-diphosphate bound as the incoming nucleotide substrate

Structural Biology Knowledgebase: 1T05 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.292
  • R-Value Work: 0.253

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1T05

Classification: Transferase / DNA

Total Structure Weight: 131188.62


Macromolecule Entities
Molecule Chains Length Organism Details
POL polyprotein A 558 Human immunodeficiency virus 1 EC#: 2.7.7.49 IUBMB
Fragment: HIV-1 reverse transcriptase p66 subunit
Mutation: Q258C, C280S
Gene Name(s): gag-pol
POL polyprotein B 437 Human immunodeficiency virus 1 EC#: 2.7.7.49 IUBMB
Fragment: HIV-1 reverse transcriptase p51 subunit
Mutation: C280S
Gene Name(s): gag-pol
Macromolecule Entities
Molecule Chains Length Organism Details
oligonucleotide template T 27 synthetic
oligonucleotide primer P 21 synthetic

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
TNV
Query on TNV

A [2-(6-AMINO-9H-PURIN-9-YL)-1-METHYLETHOXY]METHYL- TRIPHOSPHATE
TENOFOVIR-DIPHOSPHATE (Synonym)
C9 H16 N5 O10 P3
IACQCQDWSIQSRP-ZCFIWIBFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
MRG
Query on MRG
P DNA LINKING C13 H20 N5 O7 P S DG
DDG
Query on DDG
P DNA LINKING C10 H14 N5 O6 P DG

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.292
  • R-Value Work: 0.253
  • Space Group: P 31 1 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 171.57 α = 90.00
b = 171.57 β = 90.00
c = 156.27 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-04-07
  • Released Date: 2004-05-11
  • Deposition author(s): Tuske, S., Sarafianos, S.G., Ding, J., Arnold, E.

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4