1MN9

NDP kinase mutant (H122G) complex with RTP

Structural Biology Knowledgebase: 1MN9 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.207

Literature

Macromolecules
Sequence Display for 1MN9

Classification: transferase

Total Structure Weight: 50763.23

Macromolecule Entities
Molecule Chains Length Organism Details
NDP kinase A, B, C 155 Dictyostelium discoideum EC#: 2.7.4.6 IUBMB
Mutation: H122G
Gene Name(s): ndkC-1 gip17 ndkB DDB_G0273069 ndkC-2 DDB_G0273805
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A RIBAVIRIN TRIPHOSPHATE
C8 H15 N4 O14 P3
MMJOCKKLRMRSEQ-AFCXAGJDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
RTP N/A in BindingDB
N/A in BindingMoad
Kd: 24000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.207
  • Space Group: P 31 2 1

Unit Cell:

Length (Å) Angle (°)
a = 71.73 α = 90.00
b = 71.73 β = 90.00
c = 153.82 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-09-05
  • Released Date: 2003-03-18
  • Deposition author(s): Gallois-montbrun, S., Chen, Y., Dutartre, H., Morera, S., Guerreiro, C., Mulard, L., Schneider, B., Janin, J., Canard, B., Veron, M., Deville-bonne, D.

Revision History

  • 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