4MDE

Structure of bacterial polynucleotide kinase product complex bound to GDP and DNA

Structural Biology Knowledgebase: 4MDE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.206
  • R-Value Work: 0.164

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4MDE

Classification: TRANSFERASE / DNA

Total Structure Weight: 42852.04


Macromolecule Entities
Molecule Chains Length Organism Details
Metallophosphoesterase A, B 171 Ruminiclostridium thermocellum Mutation: D38N, L137M
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(P*CP*CP*TP*GP*T)-3') C, D 5 synthetic

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

A, B GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
Ligand Explorer
 
JSmol
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.206
  • R-Value Work: 0.164
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 54.44 α = 90.00
b = 73.12 β = 90.00
c = 119.04 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-08-22
  • Released Date: 2013-11-06
  • Deposition author(s): Shuman, S., Das, U., Wang, L.K., Smith, P., Jacewicz, A.

Revision History

  • 2014-02-12
    Type: Citation | Details: Citation update