1B4S

STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE H122G MUTANT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.305
  • R-Value Work: 0.203

Literature

Macromolecules
Sequence Display for 1B4S

Classification: PHOSPHOTRANSFERASE

Total Structure Weight: 51845.61

Macromolecule Entities
Molecule Chains Length Organism Details
NUCLEOSIDE DIPHOSPHATE 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 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ADP
Query on ADP

A, B, C ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A, B, C PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.305
  • R-Value Work: 0.203
  • Space Group: P 31 2 1

Unit Cell:

Length (Å) Angle (°)
a = 70.00 α = 90.00
b = 70.00 β = 90.00
c = 151.77 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1998-12-28
  • Released Date: 1999-06-15
  • Deposition author(s): Meyer, P., Janin, J.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4