4KFD

Crystal structure of Hansenula polymorpha copper amine oxidase-1 reduced by methylamine at pH 6.0

PDB DOI: https://doi.org/10.2210/pdb4KFD/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 ?
R-Value Free: 0.164
R-Value Work: 0.134
R-Value Observed: 0.136

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

Macromolecule Content

Total Structure Weight: 471.63 kDa
Atom Count: 36,394
Modelled Residue Count: 3,933
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
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain MA [auth C] SDF format, chain QB [auth F] MOL2 format, chain DA [auth B] MOL2 format, chain MA [auth C] MOL2 format, chain QB [auth F] mmCIF format, chain DA [auth B] mmCIF format, chain MA [auth C] mmCIF format, chain QB [auth F]	DA [auth B], MA [auth C], QB [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain DA [auth B] Focus chain MA [auth C] Focus chain QB [auth F] Interactions & Density Focus chain DA [auth B] Focus chain MA [auth C] Focus chain QB [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth D] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DB [auth E] SDF format, chain EA [auth B] SDF format, chain EB [auth E] SDF format, chain FB [auth E] SDF format, chain GB [auth E] SDF format, chain HA [auth C] SDF format, chain HB [auth E] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain IB [auth E] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain LB [auth F] SDF format, chain M [auth A] SDF format, chain MB [auth F] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain NB [auth F] SDF format, chain O [auth A] SDF format, chain OA [auth C] SDF format, chain OB [auth F] SDF format, chain P [auth A] SDF format, chain PA [auth C] SDF format, chain PB [auth F] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain RB [auth F] SDF format, chain S [auth A] SDF format, chain SA [auth D] SDF format, chain SB [auth F] SDF format, chain T [auth A] SDF format, chain TA [auth D] SDF format, chain TB [auth F] SDF format, chain UA [auth D] SDF format, chain UB [auth F] SDF format, chain VA [auth D] SDF format, chain W [auth B] SDF format, chain WA [auth D] SDF format, chain X [auth B] SDF format, chain XA [auth D] SDF format, chain Y [auth B] SDF format, chain YA [auth D] SDF format, chain Z [auth B] SDF format, chain ZA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DB [auth E] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth E] MOL2 format, chain FB [auth E] MOL2 format, chain GB [auth E] MOL2 format, chain HA [auth C] MOL2 format, chain HB [auth E] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain IB [auth E] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain LB [auth F] MOL2 format, chain M [auth A] MOL2 format, chain MB [auth F] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain NB [auth F] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain OB [auth F] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain PB [auth F] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain RB [auth F] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth D] MOL2 format, chain SB [auth F] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth D] MOL2 format, chain TB [auth F] MOL2 format, chain UA [auth D] MOL2 format, chain UB [auth F] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DB [auth E] mmCIF format, chain EA [auth B] mmCIF format, chain EB [auth E] mmCIF format, chain FB [auth E] mmCIF format, chain GB [auth E] mmCIF format, chain HA [auth C] mmCIF format, chain HB [auth E] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain IB [auth E] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain LB [auth F] mmCIF format, chain M [auth A] mmCIF format, chain MB [auth F] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain NB [auth F] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain OB [auth F] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain PB [auth F] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain RB [auth F] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth D] mmCIF format, chain SB [auth F] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth D] mmCIF format, chain TB [auth F] mmCIF format, chain UA [auth D] mmCIF format, chain UB [auth F] mmCIF format, chain VA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth D]	AA [auth B] AB [auth D] BA [auth B] CA [auth B] DB [auth E] AA [auth B], AB [auth D], BA [auth B], CA [auth B], DB [auth E], EA [auth B], EB [auth E], FB [auth E], GB [auth E], HA [auth C], HB [auth E], I [auth A], IA [auth C], IB [auth E], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], LB [auth F], M [auth A], MB [auth F], N [auth A], NA [auth C], NB [auth F], O [auth A], OA [auth C], OB [auth F], P [auth A], PA [auth C], PB [auth F], Q [auth A], R [auth A], RB [auth F], S [auth A], SA [auth D], SB [auth F], T [auth A], TA [auth D], TB [auth F], UA [auth D], UB [auth F], VA [auth D], W [auth B], WA [auth D], X [auth B], XA [auth D], Y [auth B], YA [auth D], Z [auth B], ZA [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DB [auth E] Focus chain EA [auth B] Focus chain EB [auth E] Focus chain FB [auth E] Focus chain GB [auth E] Focus chain HA [auth C] Focus chain HB [auth E] Focus chain I [auth A] Focus chain IA [auth C] Focus chain IB [auth E] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain LB [auth F] Focus chain M [auth A] Focus chain MB [auth F] Focus chain N [auth A] Focus chain NA [auth C] Focus chain NB [auth F] Focus chain O [auth A] Focus chain OA [auth C] Focus chain OB [auth F] Focus chain P [auth A] Focus chain PA [auth C] Focus chain PB [auth F] Focus chain Q [auth A] Focus chain R [auth A] Focus chain RB [auth F] Focus chain S [auth A] Focus chain SA [auth D] Focus chain SB [auth F] Focus chain T [auth A] Focus chain TA [auth D] Focus chain TB [auth F] Focus chain UA [auth D] Focus chain UB [auth F] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DB [auth E] Focus chain EA [auth B] Focus chain EB [auth E] Focus chain FB [auth E] Focus chain GB [auth E] Focus chain HA [auth C] Focus chain HB [auth E] Focus chain I [auth A] Focus chain IA [auth C] Focus chain IB [auth E] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain LB [auth F] Focus chain M [auth A] Focus chain MB [auth F] Focus chain N [auth A] Focus chain NA [auth C] Focus chain NB [auth F] Focus chain O [auth A] Focus chain OA [auth C] Focus chain OB [auth F] Focus chain P [auth A] Focus chain PA [auth C] Focus chain PB [auth F] Focus chain Q [auth A] Focus chain R [auth A] Focus chain RB [auth F] Focus chain S [auth A] Focus chain SA [auth D] Focus chain SB [auth F] Focus chain T [auth A] Focus chain TA [auth D] Focus chain TB [auth F] Focus chain UA [auth D] Focus chain UB [auth F] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain BB [auth E] SDF format, chain FA [auth C] SDF format, chain G [auth A] SDF format, chain JB [auth F] SDF format, chain QA [auth D] SDF format, chain U [auth B] MOL2 format, chain BB [auth E] MOL2 format, chain FA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain JB [auth F] MOL2 format, chain QA [auth D] MOL2 format, chain U [auth B] mmCIF format, chain BB [auth E] mmCIF format, chain FA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain JB [auth F] mmCIF format, chain QA [auth D] mmCIF format, chain U [auth B]	BB [auth E] FA [auth C] G [auth A] JB [auth F] QA [auth D] BB [auth E], FA [auth C], G [auth A], JB [auth F], QA [auth D], U [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain BB [auth E] Focus chain FA [auth C] Focus chain G [auth A] Focus chain JB [auth F] Focus chain QA [auth D] Focus chain U [auth B] Interactions & Density Focus chain BB [auth E] Focus chain FA [auth C] Focus chain G [auth A] Focus chain JB [auth F] Focus chain QA [auth D] Focus chain U [auth B]
PEO Query on PEO Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain KB [auth F] SDF format, chain V [auth B] SDF format, chain CB [auth E] SDF format, chain H [auth A] SDF format, chain RA [auth D] MOL2 format, chain GA [auth C] MOL2 format, chain KB [auth F] MOL2 format, chain V [auth B] MOL2 format, chain CB [auth E] MOL2 format, chain H [auth A] MOL2 format, chain RA [auth D] mmCIF format, chain GA [auth C] mmCIF format, chain KB [auth F] mmCIF format, chain V [auth B] mmCIF format, chain CB [auth E] mmCIF format, chain H [auth A] mmCIF format, chain RA [auth D]	CB [auth E] GA [auth C] H [auth A] KB [auth F] RA [auth D] CB [auth E], GA [auth C], H [auth A], KB [auth F], RA [auth D], V [auth B]	HYDROGEN PEROXIDE H₂ O₂ MHAJPDPJQMAIIY-UHFFFAOYSA-N		Interactions Focus chain CB [auth E] Focus chain GA [auth C] Focus chain H [auth A] Focus chain KB [auth F] Focus chain RA [auth D] Focus chain V [auth B] Interactions & Density Focus chain CB [auth E] Focus chain GA [auth C] Focus chain H [auth A] Focus chain KB [auth F] Focus chain RA [auth D] Focus chain V [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.69 ?
R-Value Free: 0.164
R-Value Work: 0.134
R-Value Observed: 0.136
Space Group: P 1 2₁ 1

Unit Cell:

Length ( ? )	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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-08-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-08-21
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary