2YMW

Structure of the epsilon-lysine oxidase from Marinomonas mediterranea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the Epsilon-Lysine Oxidase from Marinomonas Mediterranea

Medrano, F.J.Sanchez-Amat, A.Romero, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-LYSINE 6-OXIDASE
A, B
746Marinomonas mediterranea (strain ATCC 700492 / JCM 21426 / NBRC 103028 / MMB-1)Mutation(s): 0 
Gene Names: lodA
EC: 1.4.3.20
Find proteins for F2JXJ3 (Marinomonas mediterranea (strain ATCC 700492 / JCM 21426 / NBRC 103028 / MMB-1))
Go to UniProtKB:  F2JXJ3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EOH
Query on EOH

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Download CCD File 
A, B
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TRQ
Query on TRQ
A, B
L-PEPTIDE LINKINGC11 H10 N2 O4TRP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.192 
  • Space Group: P 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 70.680α = 90.00
b = 127.883β = 107.18
c = 106.897γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SHARPphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Source and taxonomy