3V81

Crystal structure of HIV-1 reverse transcriptase (RT) with DNA and the nonnucleoside inhibitor nevirapine

Structural Biology Knowledgebase: 3V81 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.298
  • R-Value Work: 0.250

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3V81

Classification: TRANSFERASE / DNA

Total Structure Weight: 258472.61


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
Fragment: UNP Residues 600-1153
Mutation: Q258C, C280S, D498N
Gene Name(s): gag-pol
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
DNA (5'-D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3') E, T 27 synthetic
DNA (5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(ATM))-3') F, P 21 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NVP
Query on NVP

A, C 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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
NVP EC50: 20 - >7500 nM (98) BindingDB
IC50: 60 - 160000 nM (98) BindingDB
Ki: 400 - 36000 nM (98) BindingDB

N/A in BindingMoad
N/A in PDBbind
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
MRG
Query on MRG
F, P DNA LINKING C13 H20 N5 O7 P S DG
ATM
Query on ATM
F, P DNA LINKING C10 H14 N5 O7 P DT

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.298
  • R-Value Work: 0.250
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 89.82 α = 90.00
b = 132.05 β = 100.84
c = 142.73 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-12-22
  • Released Date: 2012-01-18
  • Deposition author(s): Das, K., Martinez, S.E., Arnold, E.

Revision History

  • 2012-02-15
    Type: Citation | Details: Citation update