4B2H

COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The Flavoprotein Dodecin as a Redox Probe for Electron Transfer Through DNA.

Yu, Y.Heidel, B.Parapugna, T.L.Wenderhold-Reeb, S.Song, B.Schonherr, H.Grininger, M.Noll, G.

(2013) Angew Chem Int Ed Engl 52: 4950


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DODECINA74Halobacterium salinarum R1Mutation(s): 1 
Gene Names: OE_3073R
UniProt
Find proteins for B0R5M0 (Halobacterium salinarum (strain ATCC 29341 / DSM 671 / R1))
Explore B0R5M0 
Go to UniProtKB:  B0R5M0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0R5M0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C3F
Query on C3F

Download Ideal Coordinates CCD File 
D [auth A]3-[7,8-dimethyl-2,4-bis(oxidanylidene)benzo[g]pteridin-10-yl]propylcarbamic acid
C16 H17 N5 O4
SDVCPFDZIJESAH-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
B [auth A],
E [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.167 
  • Space Group: F 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.005α = 90
b = 142.005β = 90
c = 142.005γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection, Derived calculations, Other