7CL5

The crystal structure of KanJ in complex with kanamycin B and N-oxalylglycine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report



Literature

Stepwise Post-glycosylation Modification of Sugar Moieties in Kanamycin Biosynthesis

Eguchi, T.Kudo, F.Kitayama, Y.Miyanaga, A.Numakura, M.

(2021) Chembiochem 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kanamycin B dioxygenaseABCDEF301Streptomyces kanamyceticusMutation(s): 0 
Gene Names: kanJkacB
EC: 1.14.11.37
Find proteins for Q6L732 (Streptomyces kanamyceticus)
Explore Q6L732 
Go to UniProtKB:  Q6L732
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9CS
Query on 9CS

Download Ideal Coordinates CCD File 
A, B, C, D, E, F
(1R,2S,3S,4R,6S)-4,6-DIAMINO-3-[(3-AMINO-3-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-2-HYDROXYCYCLOHEXYL 2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSIDE
C18 H37 N5 O10
SKKLOUVUUNMCJE-FQSMHNGLSA-N
 Ligand Interaction
OGA
Query on OGA

Download Ideal Coordinates CCD File 
A, B, C, D, E, F
N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
A, B, C, D, E, F
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.083α = 90
b = 184.259β = 97.68
c = 109.771γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2021-01-13
    Type: Initial release