3JSM

K65R mutant HIV-1 reverse transcriptase cross-linked to DS-DNA and complexed with tenofovir-diphosphate as the incoming nucleotide substrate

Structural Biology Knowledgebase: 3JSM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.285
  • R-Value Work: 0.252

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3JSM

Classification: TRANSFERASE / DNA COMPLEX

Total Structure Weight: 130920.27


Macromolecule Entities
Molecule Chains Length Organism Details
HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT A 558 Human immunodeficiency virus 1 EC#: 2.7.7.49 IUBMB
Mutation: K65R, Q258C, C280S
Gene Name(s): gag-pol
HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT B 437 Human immunodeficiency virus 1 EC#: 2.7.7.49 IUBMB
Mutation: C280S
Gene Name(s): gag-pol
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*A*TP*GP*GP*TP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3') T 27 synthetic
DNA (5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(DDG))-3') 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)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
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: 0.285
  • R-Value Work: 0.252
  • Space Group: P 31 1 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 170.31 α = 90.00
b = 170.31 β = 90.00
c = 155.44 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-09-10
  • Released Date: 2009-09-29
  • Deposition author(s): Das, K., Arnold, E.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Source and taxonomy | Details: Removed strain from scientific name