3KLF

Crystal structure of wild-type HIV-1 Reverse Transcriptase crosslinked to a DSDNA with a bound excision product, AZTPPPPA

Structural Biology Knowledgebase: 3KLF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.288
  • R-Value Work: 0.264

Literature

Macromolecules
Sequence Display for 3KLF

Classification: TRANSFERASE / DNA

Total Structure Weight: 527068.94


Macromolecule Entities
Molecule Chains Length Organism Details
Reverse transcriptase/ribonuclease H A, E, I, M 557 Human immunodeficiency virus 1 EC#: 2.7.7.49 IUBMB 2.7.7.7 IUBMB 3.1.26.4 IUBMB
Mutation: Q258C, C280S
Gene Name(s): gag-pol
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
p51 RT B, F, J, N 444 Human immunodeficiency virus 1 Mutation: C280S
Gene Name(s): gag-pol
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*AP*T*GP*CP*AP*TP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3') C, G, K, O 27 synthetic DNA template
DNA (5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(2DA))-3') D, H, L, P 21 synthetic DNA primer

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZP4
Query on ZP4

A, E, I, M [[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4- dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy- hydroxy-phosphoryl]oxy-hydroxy-phosphoryl] [(2S,3S,5R)- 3-azido-5-(5-methyl-2,4-dioxo-pyrimidin-1- yl)oxolan-2-yl]methyl hydrogen phosphate
C20 H28 N10 O19 P4
NHJROJSMKQZWCP-SLFMBYJQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

A, E, I, M MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
MRG
Query on MRG
D, H, L, P DNA LINKING C13 H20 N5 O7 P S DG
2DA
Query on 2DA
D, H, L, P DNA LINKING C10 H14 N5 O5 P DA

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.288
  • R-Value Work: 0.264
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 78.53 α = 90.00
b = 274.81 β = 90.11
c = 152.37 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-11-07
  • Released Date: 2010-09-22
  • Deposition author(s): Tu, X., Das, K., Sarafianos, S.G., Arnold, E.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4