2CC6

Complexes of Dodecin with Flavin and Flavin-like Ligands


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.207

Literature

Macromolecules
Sequence Display for 2CC6

Classification: FLAVOPROTEIN

Total Structure Weight: 7887.41

Macromolecule Entities
Molecule Chains Length Organism Details
VNG1446H A 68 Halobacterium salinarum Details: LUMICHROME BOUND
Gene Name(s): VNG_1446H
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
LUM
Query on LUM

A LUMICHROME
7,8-DIMETHYLALLOXAZINE; 6,7-DIMETHYLALLOXAZINE (Synonym)
C12 H10 N4 O2
ZJTJUVIJVLLGSP-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
LUM N/A in BindingDB
Kd: 9.88 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.207
  • Space Group: F 41 3 2

Unit Cell:

Length (Å) Angle (°)
a = 141.72 α = 90.00
b = 141.72 β = 90.00
c = 141.72 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-01-12
  • Released Date: 2006-02-15
  • Deposition author(s): Grininger, M., Zeth, K., Oesterhelt, D.

Revision History

  • 2011-05-08
    Type: Version format compliance
  • 2011-07-13
    Type: Version format compliance