4JKH

Open and closed forms of D1781E human PRP8 RNase H-like domain with bound Mg ion

Structural Biology Knowledgebase: 4JKH SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.172

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4JKH

Classification: RNA BINDING PROTEIN

Total Structure Weight: 51480.61

Macromolecule Entities
Molecule Chains Length Organism Details
Pre-mRNA-processing-splicing factor 8 A, B 222 Homo sapiens Fragment: PRP8 RNase H-like domain, UNP residues 1769-1990'
Mutation: D1781E
Gene Name(s): PRPF8 Gene View PRPC8

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

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

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.172
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 75.47 α = 90.00
b = 77.74 β = 90.00
c = 94.23 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-03-09
  • Released Date: 2013-05-22
  • Deposition author(s): Schellenberg, M.J., Wu, T., Ritchie, D.B., Atta, K.A., MacMillan, A.M.

Revision History

  • 2013-06-26
    Type: Citation | Details: Citation update
  • 2013-06-19
    Type: Citation | Details: Citation update