1M5K

Crystal structure of a hairpin ribozyme in the catalytically-active conformation

Structural Biology Knowledgebase: 1M5K SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.284
  • R-Value Work: 0.229

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1M5K

Classification: TRANSLATION / RNA

Total Structure Weight: 97810.41


Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (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 21 synthetic
RNA HAIRPIN RIBOZYME B, E 92 synthetic

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

A, B, C, D, E, F CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

F CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 3 Unique
ID Chains Type Formula 2D Diagram Parent
A2M
Query on A2M
A, D RNA LINKING C11 H16 N5 O7 P A
IU
Query on IU
A, D RNA LINKING C9 H12 I N2 O9 P U
GTP
Query on GTP
B, E NON-POLYMER C10 H16 N5 O14 P3 G

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.284
  • R-Value Work: 0.229
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 256.30 α = 90.00
b = 44.10 β = 109.00
c = 102.40 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-07-09
  • Released Date: 2002-08-02
  • Deposition author(s): Rupert, P.B., Ferre-D'Amare, A.R.
  • Previous versions: 1HP6

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4