4IDK

HIV-1 reverse transcriptase with bound fragment at the 428 site

Structural Biology Knowledgebase: 4IDK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.182

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4IDK

Classification: transferase / transferase inhibitor

Total Structure Weight: 115934.09

Macromolecule Entities
Molecule Chains Length Organism Details
Reverse transcriptase/ribonuclease H A 557 Human immunodeficiency virus 1 EC#: 2.7.7.49 IUBMB 2.7.7.7 IUBMB 3.1.26.13 IUBMB
Fragment: P66 (unp residues 600-1154)
Mutation: K172A, K173A, C280S
Gene Name(s): gag-pol
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
p51 RT B 429 Human immunodeficiency virus 1 EC#: 2.7.7.49 IUBMB 2.7.7.7 IUBMB 3.1.26.13 IUBMB
Fragment: P51 (unp residues 600-1027)
Mutation: C280S
Gene Name(s): gag-pol

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
T27
Query on T27

A 4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin- 2-yl]amino}benzonitrile
Rilpivirine (Synonym)
C22 H18 N6
YIBOMRUWOWDFLG-ONEGZZNKSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
1FE
Query on 1FE

A N-(2-oxo-2,3-dihydro-1H-benzimidazol-5-yl)glycinamide
C9 H10 N4 O2
VRPBYMLDIVHQOX-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMS
Query on DMS

A, B DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.182
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 161.88 α = 90.00
b = 73.07 β = 100.48
c = 108.96 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-12-12
  • Released Date: 2013-02-06
  • Deposition author(s): Bauman, J.D., Patel, D., Arnold, E.

Revision History

  • 2015-06-17
    Type: Non-polymer description | Details: --
  • 2013-04-24
    Type: Citation | Details: Citation update