1B99

3'-FLUORO-URIDINE DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE

Structural Biology Knowledgebase: 1B99 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.304
  • R-Value Work: 0.207

Literature

Macromolecules
Sequence Display for 1B99

Classification: TRANSFERASE

Total Structure Weight: 102168.87

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE) A, B, C..., D, E, FA, B, C, D, E, F 155 Dictyostelium discoideum EC#: 2.7.4.6 IUBMB
Fragment: HEXAMER
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
FUP
Query on FUP

A 2',3'-DIDEOXY-3'-FLUORO-URIDIDINE-5'-DIPHOSPHATE
FUDP (Synonym)
C9 H13 F N2 O10 P2
WLQBZMZTRNPUDL-SHYZEUOFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
POP
Query on POP

B, C, D, E, F PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.304
  • R-Value Work: 0.207
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 70.02 α = 90.00
b = 105.31 β = 117.43
c = 70.35 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-02-22
  • Released Date: 1999-06-28
  • Deposition author(s): Janin, J., Xu, Y.

Revision History

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