488D

CATALYTIC RNA ENZYME-PRODUCT COMPLEX

Structural Biology Knowledgebase: 488D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.301
  • R-Value Work: 0.258

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 488D

Classification: RNA

Total Structure Weight: 22126.29

Macromolecule Entities
Molecule Chains Length Organism Details
RNA RIBOZYME STRAND A 16 synthetic 16-MER
FIRST RNA FRAGMENT OF CLEAVED SUBSTRATE B 20 synthetic 20-MER, 3'-END CYCLIC PHOSPHATE
SECOND RNA FRAGMENT OF CLEAVED SUBSTRATE C 5 synthetic 5-MER
UNCLEAVED RNA SUBSTRATE D 25 synthetic 25-MER

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

A, B CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CCC
Query on CCC
B RNA LINKING C9 H13 N3 O10 P2 C

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.301
  • R-Value Work: 0.258
  • Space Group: P 31 2 1

Unit Cell:

Length (Å) Angle (°)
a = 65.50 α = 90.00
b = 65.50 β = 90.00
c = 136.48 γ = 120.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2000-02-25
  • Released Date: 2000-03-06
  • Deposition author(s): Murray, J.B., Szoke, H., Szoke, A., Scott, W.G.

Revision History

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