Macromolecule Content

Total Structure Weight: 205.76 kDa
Atom Count: 13605
Residue Count: 1685
Unique protein chains: 1

7CL5

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

DOI: 10.2210/pdb7CL5/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces kanamyceticus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-07-20 Released: 2021-01-13
Deposition Author(s): Kitayama, Y., Miyanaga, A., Kudo, F., Eguchi, T.

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
Molecule	Chains	Sequence Length	Organism	Details	Image
Kanamycin B dioxygenase	A, B, C, D, E, F	301	Streptomyces kanamyceticus	Mutation(s): 0 Gene Names: kanJ, kacB 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
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9CS Query on 9CS Download Ideal Coordinates CCD File SDF format, chain I [A] SDF format, chain L [B] SDF format, chain O [C] SDF format, chain R [D] SDF format, chain U [E] SDF format, chain X [F] MOL2 format, chain I [A] MOL2 format, chain L [B] MOL2 format, chain O [C] MOL2 format, chain R [D] MOL2 format, chain U [E] MOL2 format, chain X [F]	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 SDF format, chain H [A] SDF format, chain K [B] SDF format, chain N [C] SDF format, chain Q [D] SDF format, chain T [E] SDF format, chain W [F] MOL2 format, chain H [A] MOL2 format, chain K [B] MOL2 format, chain N [C] MOL2 format, chain Q [D] MOL2 format, chain T [E] MOL2 format, chain W [F]	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 SDF format, chain G [A] SDF format, chain J [B] SDF format, chain M [C] SDF format, chain P [D] SDF format, chain S [E] SDF format, chain V [F] MOL2 format, chain G [A] MOL2 format, chain J [B] MOL2 format, chain M [C] MOL2 format, chain P [D] MOL2 format, chain S [E] MOL2 format, chain V [F]	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 = 50.083	α = 90
b = 184.259	β = 97.68
c = 109.771	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2020-07-20
Released Date: 2021-01-13

Deposition Author(s):

Revision History

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

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.