4KCF

X-ray Structure of a KijD3 in Complex with FMN and dTDP-3-amino-2,3,6-trideoxy-4-keto-3-methyl-D-glucose

Structural Biology Knowledgebase: 4KCF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.175

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4KCF

Classification: OXIDOREDUCTASE

Total Structure Weight: 49345.59

Macromolecule Entities
Molecule Chains Length Organism Details
FAD-dependent oxidoreductase A 454 Actinomadura kijaniata Gene Name(s): KijD3
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A [(2R,4S,6R)-4-azanyl-4,6-dimethyl-5,5-bis(oxidanyl)oxan- 2-yl] [[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin- 1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl- phosphoryl] hydrogen phosphate
3, (Synonym)
C17 H29 N3 O14 P2
GACNZVKWDHTCBB-HHMBNNFFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FMN
Query on FMN

A FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE (Synonym)
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.175
  • Space Group: I 2 2 2

Unit Cell:

Length (Å) Angle (°)
a = 70.83 α = 90.00
b = 81.30 β = 90.00
c = 152.63 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-04-24
  • Released Date: 2013-05-22
  • Deposition author(s): Holden, H.M., Thoden, J.B., Branch, M.C., Zimmer, A.L., Bruender, N.A.

Revision History

  • 2013-12-18
    Type: Citation | Details: Citation update
  • 2013-05-29
    Type: Atom nomenclature | Details: AKM atom nomenclature corrected
  • 2013-05-29
    Type: Non-polymer description | Details: AKM name corrected