5WX2

Crystal structure of porcine kidney D-amino acid oxidase mutant (I230A/R283G)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.169 

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

Tailoring D-amino acid oxidase from the pid kidney to R-stereoselective amine oxidase and its use in the deracemization of 4-chlorobenzhydrylamine

Yasukawa, K.Motojima, F.Ohno, A.Asano, Y.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-amino-acid oxidase
A, B, C, D, E
A, B, C, D, E, F, G, H
347Sus scrofaMutation(s): 2 
Gene Names: DAO
EC: 1.4.3.3
UniProt
Find proteins for P00371 (Sus scrofa)
Explore P00371 
Go to UniProtKB:  P00371
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00371
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
BA [auth E]
EA [auth F]
I [auth A]
KA [auth G]
O [auth B]
BA [auth E],
EA [auth F],
I [auth A],
KA [auth G],
O [auth B],
OA [auth H],
T [auth C],
W [auth D]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
CA [auth E]
FA [auth F]
GA [auth F]
HA [auth F]
IA [auth F]
CA [auth E],
FA [auth F],
GA [auth F],
HA [auth F],
IA [auth F],
J [auth A],
K [auth A],
L [auth A],
LA [auth G],
M [auth A],
MA [auth G],
NA [auth G],
P [auth B],
PA [auth H],
Q [auth B],
QA [auth H],
R [auth B],
S [auth B],
U [auth C],
X [auth D],
Y [auth D],
Z [auth D]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D]
DA [auth E]
JA [auth F]
N [auth A]
RA [auth H]
AA [auth D],
DA [auth E],
JA [auth F],
N [auth A],
RA [auth H],
V [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.169 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.402α = 90
b = 270.896β = 90
c = 135.429γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JST, ERATOJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description