4PQU

Crystal structure of HIV-1 Reverse Transcriptase in complex with RNA/DNA and dATP

Structural Biology Knowledgebase: 4PQU SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.202

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4PQU

Classification: TRANSFERASE HYDROLASE / DNA / RNA

Total Structure Weight: 260479.63


Macromolecule Entities
Molecule Chains Length Organism Details
HIV-1 Reverse Transcriptase, p66 subunit A, C 556 Human immunodeficiency virus 1 EC#: 2.7.7.49 IUBMB 2.7.7.7 IUBMB 3.1.13.2 IUBMB 3.1.26.13 IUBMB
Fragment: UNP residues 600-1153
Mutation: Q258C, C280S, D498N
Gene Name(s): gag-pol
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
HIV-1 Reverse Transcriptase, p51 subunit B, D 428 Human immunodeficiency virus 1 EC#: 2.7.7.49 IUBMB 2.7.7.7 IUBMB
Fragment: UNP residues 600-1027
Mutation: C280S
Gene Name(s): gag-pol
Macromolecule Entities
Molecule Chains Length Organism Details
5'-R(*AP*UP*GP*GP*UP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*UP*GP*UP*G)-3' E, T 27 synthetic
5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*G)-3' F, P 21 synthetic

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DTP
Query on DTP

A, C 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B, C, D SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, C MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.202
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 89.44 α = 90.00
b = 128.29 β = 101.76
c = 130.68 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-03-04
  • Released Date: 2014-06-18
  • Deposition author(s): Das, K., Bandwar, R.P., Arnold, E.

Revision History

  • 2014-07-16
    Type: Citation | Details: Citation update