1PAE

nucleoside diphosphate kinase

Structural Biology Knowledgebase: 1PAE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.182

Literature

Macromolecules
Sequence Display for 1PAE

Classification: TRANSFERASE

Total Structure Weight: 17127.00

Macromolecule Entities
Molecule Chains Length Organism Details
Nucleoside diphosphate kinase, cytosolic X 155 Dictyostelium discoideum EC#: 2.7.4.6 IUBMB
Mutation: M1M, M80M, M94M, H122U
Gene Name(s): ndkC-1 gip17 ndkB DDB_G0273069 ndkC-2 DDB_G0273805
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

X SELENIUM ATOM
Se
SPVXKVOXSXTJOY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
X L-PEPTIDE LINKING C5 H11 N O2 Se MET
SEC
Query on SEC
L-PEPTIDE LINKING C3 H7 N O2 Se --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.182
  • Space Group: P 63 2 2

Unit Cell:

Length (Å) Angle (°)
a = 76.63 α = 90.00
b = 76.63 β = 90.00
c = 106.51 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-05-14
  • Released Date: 2003-11-11
  • Deposition author(s): Strub, M.-P., Hoh, F., Sanchez, J.-F., Strub, J.M., Bock, A., Aumelas, A., Dumas, C.

Revision History

  • 2014-08-06
    Type: Linkage | Details: Remove backbone links to SEC
  • 2014-08-06
    Type: Polymer description | Details: Use one letter code for SEC
  • 2014-02-19
    Type: Polymer description | Details: Change CSE to SEC
  • 2014-02-19
    Type: Atom nomenclature | Details: Change CSE to SEC
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values