4EV5

Crystal structure of copper amine oxidase-1 from Hansenula polymorpha in complex with benzylamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of copper amine oxidase-1 from Hansenula polymorpha in complex with benzylamine

Klema, V.J.Solheid, C.J.Klinman, J.P.Wilmot, C.M.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisomal primary amine oxidase
A, B, C, D, E
A, B, C, D, E, F
692Ogataea angustaMutation(s): 0 
Gene Names: AMO
EC: 1.4.3.21
UniProt
Find proteins for P12807 (Pichia angusta)
Explore P12807 
Go to UniProtKB:  P12807
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12807
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ABN
Query on ABN

Download Ideal Coordinates CCD File 
EA [auth C]
KA [auth D]
N [auth A]
RA [auth E]
W [auth B]
EA [auth C],
KA [auth D],
N [auth A],
RA [auth E],
W [auth B],
ZA [auth F]
BENZYLAMINE
C7 H9 N
WGQKYBSKWIADBV-UHFFFAOYSA-N
GOL
Query on GOL

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AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
G [auth A]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
G [auth A],
GA [auth D],
HA [auth D],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
K [auth A],
L [auth A],
MA [auth E],
NA [auth E],
O [auth B],
OA [auth E],
Q [auth B],
QA [auth E],
R [auth B],
S [auth B],
T [auth B],
TA [auth F],
U [auth B],
UA [auth F],
VA [auth F],
WA [auth F],
XA [auth F],
Y [auth C],
Z [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU
Query on CU

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FA [auth D]
H [auth A]
LA [auth E]
P [auth B]
SA [auth F]
FA [auth D],
H [auth A],
LA [auth E],
P [auth B],
SA [auth F],
X [auth C]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
PEO
Query on PEO

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M [auth A],
PA [auth E],
V [auth B],
YA [auth F]
HYDROGEN PEROXIDE
H2 O2
MHAJPDPJQMAIIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TYQ
Query on TYQ
A, B, C, D, E
A, B, C, D, E, F
L-PEPTIDE LINKINGC9 H12 N2 O4TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.239α = 90
b = 233.706β = 96.57
c = 105.045γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-13
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description