5LNJ

XenA - reduced - Y183F variant in complex with 7-hydroxycoumarin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.127 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Redox-dependent substrate-cofactor interactions in the Michaelis-complex of a flavin-dependent oxidoreductase

Werther, T.Wahlefeld, S.Salewski, J.Kuhlmann, U.Zebger, I.Hildebrandt, P.Dobbek, H.

(2017) Nat Commun 8: 16084


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:flavin oxidoreductase360Pseudomonas putidaMutation(s): 1 
Gene Names: O999_23785
UniProt
Find proteins for A0A1X0ZT96 (Pseudomonas putida)
Explore A0A1X0ZT96 
Go to UniProtKB:  A0A1X0ZT96
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1X0ZT96
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FNR
Query on FNR

Download Ideal Coordinates CCD File 
B [auth A]1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL
C17 H23 N4 O9 P
YTNIXZGTHTVJBW-SCRDCRAPSA-N
07L
Query on 07L

Download Ideal Coordinates CCD File 
C [auth A]7-hydroxy-2H-chromen-2-one
C9 H6 O3
ORHBXUUXSCNDEV-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.127 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.62α = 90
b = 83.46β = 90
c = 156.87γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description