2HVR

Structure of T4 RNA Ligase 2 with Nicked 5'-Adenylated nucleic acid duplex containing a 3'-deoxyribonucleotide at the nick


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.295
  • R-Value Work: 0.236

Literature

Macromolecules
Sequence Display for 2HVR

Classification: LIGASE / RNA / DNA

Total Structure Weight: 106163.67


Macromolecule Entities
Molecule Chains Length Organism Details
T4 RNA ligase 2 A, B 335 Enterobacteria phage t4 sensu lato EC#: 6.5.1.3 IUBMB
Mutation: C112G
Gene Name(s): Y10A 24.1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*TP*TP*G)-3' C, F 24 synthetic
5'-D(*CP*AP*AP*TP*TP*GP*CP*GP*AP*C)-R(P*(OMC)P*C)-3' D, G 12 synthetic
5'-R(P*A)-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*T)-3' E, H 13 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BTB
Query on BTB

A, C, F 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL- PROPANE-1,3-DIOL
BIS-TRIS BUFFER (Synonym)
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
OMC
Query on OMC
D, G RNA LINKING C10 H16 N3 O8 P C
O2C
Query on O2C
D, G RNA LINKING C9 H14 N3 O7 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.295
  • R-Value Work: 0.236
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 83.57 α = 90.00
b = 106.16 β = 90.00
c = 125.33 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-07-30
  • Released Date: 2006-10-17
  • Deposition author(s): Nandakumar, J., Lima, C.D.

Revision History

  • Version 1_0: 2006-10-17

    Type: Initial release

  • Version 1_1: 2008-05-01

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance