4KFE

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

• PDB DOI: https://doi.org/10.2210/pdb4KFE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Ogataea angusta
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2013-04-26 Released: 2013-08-21 
• Deposition Author(s): Johnson, B.J., Yukl, E.T., Klema, V.J., Wilmot, C.M.

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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 

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 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 471.72 kDa 
• Atom Count: 36,172 
• Modelled Residue Count: 3,940 
• Deposited Residue Count: 4,152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisomal primary amine oxidase	A, B, C, D, E, F	692	Ogataea angusta	Mutation(s): 0  Gene Names: AMO EC: 1.4.3.21
UniProt
Find proteins for P12807 (Pichia angusta) Explore P12807  Go to UniProtKB:  P12807

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	HA [auth B], QA [auth C], UB [auth F]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	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	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	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	I [auth A], UA [auth D], Y [auth B]	FORMYL GROUP C H2 O WSFSSNUMVMOOMR-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYY	A, B, C, D, E, F	L-PEPTIDE LINKING	C9 H10 N2 O4		TYR

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 = 103.577	α = 90
b = 222.836	β = 95.87
c = 103.619	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-21 
Deposition Author(s): Johnson, B.J., Yukl, E.T., Klema, V.J., Wilmot, C.M.

Revision History  

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