2C5U

T4 RNA Ligase (Rnl1) Crystal Structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.198

Literature

Macromolecules
Sequence Display for 2C5U

Classification: LIGASE

Total Structure Weight: 90031.13

Macromolecule Entities
Molecule Chains Length Organism Details
RNA LIGASE A, B 375 Enterobacteria phage t4 sensu lato EC#: 6.5.1.3 IUBMB
Fragment: NUCLEOTIDYL TRANSFERASE DOMAIN, RNA BINDING DOMAIN
Gene Name(s): 63
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
APC
Query on APC

A, B DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE (Synonym)
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

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

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

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.198
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 105.05 α = 90.00
b = 39.87 β = 117.27
c = 108.54 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-11-01
  • Released Date: 2005-11-04
  • Deposition author(s): El Omari, K., Ren, J., Bird, L.E., Bona, M.K., Klarmann, G., LeGrice, S.F.J., Stammers, D.K.

Revision History

  • Version 1_0: 2005-11-04

    Type: Initial release

  • Version 1_1: 2012-09-12

    Type: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance