4Q0B

Crystal structure of HIV-1 reverse transcriptase in complex with gap-RNA/DNA and Nevirapine

Structural Biology Knowledgebase: 4Q0B SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.317
  • R-Value Work: 0.235

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4Q0B

Classification: TRANSFERASE HYDROLASE / RNA / DNA / INHIBITOR

Total Structure Weight: 258467.60


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 3.1.13.2 IUBMB 3.1.26.13 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
5'-R(*AP*UP*GP*GP*UP*CP*GP*GP*CP*GP*CP*CP*CP*G)-3' E, T 14 synthetic gap-RNA template
5'-R(P*AP*CP*AP*GP*GP*GP*AP*CP*UP*GP*UP*G)-3' e, t 12 synthetic gap-RNA template
5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*G)-3' F, P 21 synthetic DNA primer

Small Molecules
Ligands 3 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)
SO4
Query on SO4

e SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, C MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.317
  • R-Value Work: 0.235
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 89.72 α = 90.00
b = 131.05 β = 100.69
c = 141.63 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-04-01
  • Released Date: 2014-06-18
  • Deposition author(s): Das, K., Martinez, S.E., Arnold, E.

Revision History

  • 2014-07-16
    Type: Citation | Details: Citation update