2FD0

HIV-1 DIS kissing-loop in complex with lividomycin

Structural Biology Knowledgebase: 2FD0 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.245

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2FD0

Classification: RNA

Total Structure Weight: 16646.24

Macromolecule Entities
Molecule Chains Length Organism Details
HIV-1 DIS RNA A, B 23 synthetic

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

A, B (2R,3S,4S,5S,6R)-2-((2S,3S,4R,5R,6R)-5-AMINO- 2-(AMINOMETHYL)-6-((2R,3S,4R,5S)-5-((1R,2R,3S,5R,6S)- 3,5-DIAMINO-2-((2S,3R,5S,6R)-3-AMINO-5-HYDROXY- 6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)- 6-HYDROXYCYCLOHEXYLOXY)-4-HYDROXY-2-(HYDROXYMETHYL)- TETRAHYDROFURAN-3-YLOXY)-4-HYDROXY-TETRAHYDRO- 2H-PYRAN-3-YLOXY)-6-(HYDROXYMETHYL)-TETRAHYDRO- 2H-PYRAN-3,4,5-TRIOL
4)-O-2, (Synonym)
C29 H55 N5 O18
DBLVDAUGBTYDFR-SWMBIRFSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A, B POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
5BU
Query on 5BU
A, B RNA LINKING C9 H12 Br N2 O9 P U

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.245
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 27.14 α = 90.00
b = 115.33 β = 90.00
c = 95.25 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2005-12-13
  • Released Date: 2006-05-16
  • Deposition author(s): Ennifar, E., Paillart, J.C., Marquet, R., Dumas, P.

Revision History

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