2GQ4

Crystal structure of an RNA racemate

Structural Biology Knowledgebase: 2GQ4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Observed: 0.241

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2GQ4

Classification: RNA

Total Structure Weight: 10562.94

Macromolecule Entities
Molecule Chains Length Organism Details
RNA (5'-R(*(0C)P*(0U)P*(0G)P*(0G)P*(0G)P*(0C)P*(0G)P*(0G))-3') K, M 8 synthetic
RNA (5'-R(*(0C)P*(0C)P*(0G)P*(0C)P*(0C)P*(0U)P*(0G)P*(0G))-3') L, N 8 synthetic

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

N GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

L, M, N CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 3 Unique
ID Chains Type Formula 2D Diagram Parent
0C
Query on 0C
K, L, M, N L-RNA LINKING C9 H14 N3 O8 P --
0U
Query on 0U
K, L, M, N L-RNA LINKING C9 H13 N2 O9 P --
0G
Query on 0G
K, L, M, N L-RNA LINKING C10 H14 N5 O8 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Observed: 0.241
  • Space Group: P -1

Unit Cell:

Length (Å) Angle (°)
a = 26.93 α = 112.25
b = 38.16 β = 101.56
c = 45.90 γ = 92.20

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2006-04-20
  • Released Date: 2006-06-27
  • Deposition author(s): Rypniewski, W., Vallazza, M., Perbandt, M., Klussmann, S., Betzel, C., Erdmann, V.A.

Revision History

  • 2012-03-28
    Type: Other | Details: space group changed from P1- to P-1
  • 2011-07-13
    Type: Polymer description | Details: change residue name, link
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update, Ligand chemistry