4EV5

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.

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
View more details

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.

Macromolecule Content

Total Structure Weight: 469.9 kDa
Atom Count: 34,660
Modelled Residue Count: 3,928
Deposited Residue Count: 4,152
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisomal primary amine oxidase	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12807
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ABN Query on ABN Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain KA [auth D] SDF format, chain N [auth A] SDF format, chain RA [auth E] SDF format, chain W [auth B] SDF format, chain ZA [auth F] MOL2 format, chain EA [auth C] MOL2 format, chain KA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain RA [auth E] MOL2 format, chain W [auth B] MOL2 format, chain ZA [auth F] mmCIF format, chain EA [auth C] mmCIF format, chain KA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain RA [auth E] mmCIF format, chain W [auth B] mmCIF format, chain ZA [auth F]	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		Interactions Focus chain EA [auth C] Focus chain KA [auth D] Focus chain N [auth A] Focus chain RA [auth E] Focus chain W [auth B] Focus chain ZA [auth F] Interactions & Density Focus chain EA [auth C] Focus chain KA [auth D] Focus chain N [auth A] Focus chain RA [auth E] Focus chain W [auth B] Focus chain ZA [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain MA [auth E] SDF format, chain NA [auth E] SDF format, chain O [auth B] SDF format, chain OA [auth E] SDF format, chain Q [auth B] SDF format, chain QA [auth E] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain TA [auth F] SDF format, chain U [auth B] SDF format, chain UA [auth F] SDF format, chain VA [auth F] SDF format, chain WA [auth F] SDF format, chain XA [auth F] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain NA [auth E] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain VA [auth F] MOL2 format, chain WA [auth F] MOL2 format, chain XA [auth F] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain MA [auth E] mmCIF format, chain NA [auth E] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth F] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth F] mmCIF format, chain VA [auth F] mmCIF format, chain WA [auth F] mmCIF format, chain XA [auth F] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	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		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain G [auth A] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain O [auth B] Focus chain OA [auth E] Focus chain Q [auth B] Focus chain QA [auth E] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain TA [auth F] Focus chain U [auth B] Focus chain UA [auth F] Focus chain VA [auth F] Focus chain WA [auth F] Focus chain XA [auth F] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain G [auth A] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain O [auth B] Focus chain OA [auth E] Focus chain Q [auth B] Focus chain QA [auth E] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain TA [auth F] Focus chain U [auth B] Focus chain UA [auth F] Focus chain VA [auth F] Focus chain WA [auth F] Focus chain XA [auth F] Focus chain Y [auth C] Focus chain Z [auth C]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain H [auth A] SDF format, chain LA [auth E] SDF format, chain P [auth B] SDF format, chain SA [auth F] SDF format, chain X [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain P [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain X [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain P [auth B] mmCIF format, chain SA [auth F] mmCIF format, chain X [auth C]	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		Interactions Focus chain FA [auth D] Focus chain H [auth A] Focus chain LA [auth E] Focus chain P [auth B] Focus chain SA [auth F] Focus chain X [auth C] Interactions & Density Focus chain FA [auth D] Focus chain H [auth A] Focus chain LA [auth E] Focus chain P [auth B] Focus chain SA [auth F] Focus chain X [auth C]
PEO Query on PEO Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain PA [auth E] SDF format, chain V [auth B] SDF format, chain YA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain YA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain PA [auth E] mmCIF format, chain V [auth B] mmCIF format, chain YA [auth F]	M [auth A], PA [auth E], V [auth B], YA [auth F]	HYDROGEN PEROXIDE H₂ O₂ MHAJPDPJQMAIIY-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain PA [auth E] Focus chain V [auth B] Focus chain YA [auth F] Interactions & Density Focus chain M [auth A] Focus chain PA [auth E] Focus chain V [auth B] Focus chain YA [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYQ Query on TYQ	A, B, C, D, E 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
R-Value Work: 0.169
R-Value Observed: 0.172
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-03-13

Deposition Author(s):

Klema, V.J.

Solheid, C.J.

Wilmot, C.M.

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