3BBF

Crystal structure of the NM23-H2 transcription factor complex with GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.196

Literature

Macromolecules
Sequence Display for 3BBF

Classification: TRANSFERASE

Total Structure Weight: 106270.70

Macromolecule Entities
Molecule Chains Length Organism Details
Nucleoside diphosphate kinase B A, B, C..., D, E, FA, B, C, D, E, F 151 Homo sapiens EC#: 2.7.4.6 IUBMB
Gene Name(s): NME2 Gene View NM23B
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D, E, F GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DTT
Query on DTT

B, F 2,3-DIHYDROXY-1,4-DITHIOBUTANE
1,4-DITHIOTHREITOL (Synonym)
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C, D, E, F MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
GDP N/A in BindingDB
N/A in BindingMoad
Kd: 5200 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.196
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 69.75 α = 90.00
b = 86.78 β = 90.00
c = 159.12 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-11-09
  • Released Date: 2008-09-23
  • Deposition author(s): Weichsel, A., Montfort, W.R.

Revision History

  • Version 1_0: 2008-09-23

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance