4B3O

Structures of HIV-1 RT and RNA-DNA Complex Reveal a Unique RT Conformation and Substrate Interface

Structural Biology Knowledgebase: 4B3O SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.295
  • R-Value Work: 0.275

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4B3O

Classification: HYDROLASE / DNA / RNA

Total Structure Weight: 132112.08


Macromolecule Entities
Molecule Chains Length Organism Details
REVERSE TRANSCRIPTASE/RIBONUCLEASE H A 560 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 3.4.23.16 IUBMB
Mutation: S68G, R83K, I411V, N447S, R461K, Y483H, V559I
Gene Name(s): gag-pol
P51 RT B 441 Human immunodeficiency virus 1 EC#: 2.7.7.49 IUBMB 2.7.7.7 IUBMB 3.1.26.13 IUBMB 3.4.23.16 IUBMB
Mutation: S68G, R83K, I411V
Gene Name(s): gag-pol
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*CP*GP*TP*AP*TP*GP*CP*CP*TP*AP*TP*AP*GP*TP *TP*AP*TP*TP*GP*TP*GP*GP*CP*C)-3' D 24 Synthetic construct
5'-R(*AP*UP*GP*AP*3DRP*GP*GP*CP*CP*AP*CP*AP*AP*UP*AP *AP*CP*UP*AP*UP*AP*GP*GP*CP*AP*UP*A)-3' R 27 Synthetic construct

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

D, R CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
EFZ
Query on EFZ

A (-)-6-CHLORO-4-CYCLOPROPYLETHYNYL-4-TRIFLUOROMETHYL- 1,4-DIHYDRO-2H-3,1-BENZOXAZIN-2-ONE
DMP-266; Efavirenz (Synonym)
C14 H9 Cl F3 N O2
XPOQHMRABVBWPR-ZDUSSCGKSA-N
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
EFZ EC50: 1 - 300 nM (98) BindingDB
IC50: 0.75 - 2100 nM (98) BindingDB
Ki: 3 - 300 nM (98) BindingDB

N/A in BindingMoad
N/A in PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
3DR
Query on 3DR
R DNA LINKING C5 H11 O6 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.295
  • R-Value Work: 0.275
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 164.60 α = 90.00
b = 164.60 β = 90.00
c = 129.03 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-07-25
  • Released Date: 2013-01-16
  • Deposition author(s): Lapkouski, M., Tian, L., Miller, J.T., Le Grice, S.F.J., Yang, W.

Revision History

  • 2013-02-20
    Type: Citation | Details: JRNL
  • 2013-01-23
    Type: Citation | Details: JRNL