4EV5 | pdb_00004ev5

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

• PDB DOI: https://doi.org/10.2210/pdb4EV5/pdb

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


• Deposited: 2012-04-25 Released: 2013-03-13 
• Deposition Author(s): Klema, V.J., Solheid, C.J., Wilmot, C.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.230 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

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.

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)

Biological Assembly 4  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 469.9 kDa 
• Atom Count: 34,660 
• Modeled Residue Count: 3,928 
• 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ABN	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	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	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	M [auth A], PA [auth E], V [auth B], YA [auth F]	HYDROGEN PEROXIDE H2 O2 MHAJPDPJQMAIIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYQ	A, B, C, D, E, F	L-PEPTIDE LINKING	C9 H12 N2 O4		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.230 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.239	α = 90
b = 233.706	β = 96.57
c = 105.045	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-13 
Deposition Author(s): Klema, V.J., Solheid, C.J., Wilmot, C.M.

Revision History  

• Version 1.0: 2013-03-13
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-27
  Changes: Structure summary