1M5V

Transition State Stabilization by a Catalytic RNA

Structural Biology Knowledgebase: 1M5V SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.221

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1M5V

Classification: TRANSLATION / RNA

Total Structure Weight: 97450.29


Macromolecule Entities
Molecule Chains Length Organism Details
U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A C, F 100 Homo sapiens Fragment: U1A RNA BINDING DOMAIN
Mutation: Y31H, Q36R
Gene Name(s): SNRPA Gene View
Macromolecule Entities
Molecule Chains Length Organism Details
RNA INHIBITOR SUBSTRATE A, D 12 synthetic first fragment
RNA INHIBITOR SUBSTRATE M, P 9 synthetic second fragment
RNA HAIRPIN RIBOZYME B, E 92 synthetic

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

C, F (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

B, C, D, E, P CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
A23
Query on A23
A, D RNA LINKING C10 H13 N5 O9 P2 A

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.221
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 258.65 α = 90.00
b = 44.26 β = 107.69
c = 102.17 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-07-09
  • Released Date: 2002-10-12
  • Deposition author(s): Rupert, P.B., Massey, A.P., Sigurdsson, S.T., Ferre-D'Amare, A.R.

Revision History

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