2HNY

Crystal Structure of E138K Mutant HIV-1 Reverse Transcriptase in Complex with Nevirapine

Structural Biology Knowledgebase: 2HNY SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.284
  • R-Value Work: 0.214

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2HNY

Classification: TRANSFERASE

Total Structure Weight: 111944.56

Macromolecule Entities
Molecule Chains Length Organism Details
Reverse transcriptase/ribonuclease H A 534 Human immunodeficiency virus 1 EC#: 2.7.7.49 IUBMB
Fragment: P66
Mutation: E138K, C280X
Gene Name(s): gag-pol
Reverse transcriptase/ribonuclease H B 422 Human immunodeficiency virus 1 EC#: 2.7.7.49 IUBMB
Fragment: P51
Mutation: E138K
Gene Name(s): gag-pol

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

A 11-CYCLOPROPYL-5,11-DIHYDRO-4-METHYL-6H-DIPYRIDO[3,2- B:2',3'-E][1,4]DIAZEPIN-6-ONE
NON-NUCLEOSIDE RT INHIBITOR NEVIRAPINE (Synonym)
C15 H14 N4 O
NQDJXKOVJZTUJA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
NVP EC50: 20 - >7500 nM (99) BindingDB
IC50: 2.6 - 23000 nM (94 - 99) BindingDB
Ki: 400 - 36000 nM (99) BindingDB

IC50: 1165 nM  BindingMOAD
IC50: 1165 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CSD
Query on CSD
A L-PEPTIDE LINKING C3 H7 N O4 S CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.284
  • R-Value Work: 0.214
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 139.60 α = 90.00
b = 115.00 β = 90.00
c = 65.60 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-07-13
  • Released Date: 2006-09-05
  • Deposition author(s): Ren, J., Nichols, C.E., Stamp, A., Chamberlain, P.P., Stammers, D.K.

Revision History

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