4KFE

Crystal structure of Hansenula polymorpha copper amine oxidase-1 reduced by methylamine at pH 7.0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.132 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural evidence for the semiquinone in a copper amine oxidase from Hansenula polymorpha: implications for the catalytic mechanism

Johnson, B.J.Yukl, E.T.Klema, V.J.Klinman, J.P.Wilmot, C.M.

(2013) J Biol Chem 


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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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HA [auth B],
QA [auth C],
UB [auth F]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

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AA [auth B]
AB [auth D]
BA [auth B]
BB [auth D]
CA [auth B]
AA [auth B],
AB [auth D],
BA [auth B],
BB [auth D],
CA [auth B],
CB [auth D],
DA [auth B],
DB [auth D],
EA [auth B],
EB [auth D],
FA [auth B],
GA [auth B],
HB [auth E],
IA [auth B],
IB [auth E],
J [auth A],
JB [auth E],
K [auth A],
KB [auth E],
L [auth A],
LA [auth C],
LB [auth E],
M [auth A],
MA [auth C],
N [auth A],
NA [auth C],
O [auth A],
OA [auth C],
OB [auth F],
P [auth A],
PA [auth C],
PB [auth F],
Q [auth A],
QB [auth F],
R [auth A],
RA [auth C],
RB [auth F],
S [auth A],
SA [auth C],
SB [auth F],
T [auth A],
TB [auth F],
U [auth A],
V [auth A],
VB [auth F],
WA [auth D],
WB [auth F],
XA [auth D],
XB [auth F],
YA [auth D],
Z [auth B],
ZA [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU
Query on CU

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FB [auth E]
G [auth A]
JA [auth C]
MB [auth F]
VA [auth D]
FB [auth E],
G [auth A],
JA [auth C],
MB [auth F],
VA [auth D],
W [auth B]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
PEO
Query on PEO

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GB [auth E]
H [auth A]
KA [auth C]
NB [auth F]
TA [auth D]
GB [auth E],
H [auth A],
KA [auth C],
NB [auth F],
TA [auth D],
X [auth B]
HYDROGEN PEROXIDE
H2 O2
MHAJPDPJQMAIIY-UHFFFAOYSA-N
FOR
Query on FOR

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I [auth A],
UA [auth D],
Y [auth B]
FORMYL GROUP
C H2 O
WSFSSNUMVMOOMR-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TYY
Query on TYY
A, B, C, D, E
A, B, C, D, E, F
L-PEPTIDE LINKINGC9 H10 N2 O4TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.132 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.577α = 90
b = 222.836β = 95.87
c = 103.619γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary