1YKV

Crystal structure of the Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene

Structural Biology Knowledgebase: 1YKV SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.262
  • R-Value Work: 0.228

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1YKV

Classification: RNA

Total Structure Weight: 32440.21

Macromolecule Entities
Molecule Chains Length Organism Details
Diels-Alder ribozyme A, C 11 synthetic 11-mer
Diels-Alder ribozyme B, D 38 synthetic 38-mer

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

A, C (3AS,9AS)-2-PENTYL-4-HYDROXYMETHYL-3A,4,9,9A- TETRAHYDRO-4,9[1',2']-BENZENO-1H-BENZ[F]ISOINDOLE- 1,3(2H)-DIONE
(11S,12S)-9-HYDROXYMETHYL-11,12-(2-PENTYL- 1,3-DIOXO-2-AZAPROPANO)-9,10-DIHYDRO-9,10- ETHANOANTHRACENE (Synonym)
C24 H25 N O3
ZXWOIFZYPFUNNQ-VMIIQTFKSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

B, D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DAI N/A in BindingDB
N/A in BindingMoad
Kd: 10000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.262
  • R-Value Work: 0.228
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 78.29 α = 90.00
b = 44.04 β = 106.87
c = 80.00 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2005-01-18
  • Released Date: 2005-02-22
  • Deposition author(s): Serganov, A., Keiper, S., Malinina, L., Tereshko, V., Skripkin, E., Hobartner, C., Polonskaia, A., Phan, A.T., Wombacher, R., Micura, R., Dauter, Z., Jaschke, A., Patel, D.J.

Revision History

  • 2011-07-13
    Type: Refinement description | Details: Fixed TLS group
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor