2IC3

Crystal Structure of K103N/Y181C Mutant HIV-1 Reverse Transcriptase (RT) in Complex with Nonnucleoside Inhibitor HBY 097

Structural Biology Knowledgebase: 2IC3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.310
  • R-Value Work: 0.257

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2IC3

Classification: Transferase

Total Structure Weight: 116793.14

Macromolecule Entities
Molecule Chains Length Organism Details
Reverse transcriptase/ribonuclease H (p66 RT) A 560 Human immunodeficiency virus 1 EC#: 2.7.7.49 IUBMB
Fragment: p66
Mutation: K103N, Y181C, C280S
Gene Name(s): gag-pol
Reverse transcriptase/ribonuclease H (p51 RT) B 447 Human immunodeficiency virus 1 EC#: 2.7.7.49 IUBMB
Fragment: p51
Mutation: K103N, Y181C, C280S
Gene Name(s): gag-pol

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

A (S)-4-ISOPROPOXYCARBONYL-6-METHOXY-3-METHYLTHIOMETHYL- 3,4-DIHYDROQUINOXALIN-2(1H)-THIONE
HBY 097 (Synonym)
C15 H20 N2 O3 S2
GWKIPRVERALPRD-ZDUSSCGKSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
HBY IC50: 8 - 56 nM (98) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.310
  • R-Value Work: 0.257
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 223.21 α = 90.00
b = 67.61 β = 108.39
c = 103.58 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-09-12
  • Released Date: 2006-12-19
  • Deposition author(s): Das, K., Arnold, E.

Revision History

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