1ekm

CRYSTAL STRUCTURE AT 2.5 A RESOLUTION OF ZINC-SUBSTITUTED COPPER AMINE OXIDASE OF HANSENULA POLYMORPHA EXPRESSED IN ESCHERICHIA COLI

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

COPPER AMINE OXIDASE

Pichia angusta

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 6	ZINC ION × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AMO_PICAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–656； UniProt 17–672 Author chain B； PDBConstruct 1–656； UniProt 17–672 Author chain C； PDBConstruct 1–656； UniProt 17–672

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1ekm
Deposition date deposition_date	2000-03-09
Structure title title	CRYSTAL STRUCTURE AT 2.5 A RESOLUTION OF ZINC-SUBSTITUTED COPPER AMINE OXIDASE OF HANSENULA POLYMORPHA EXPRESSED IN ESCHERICHIA COLI
Keywords keywords	amine oxidase, quinoprotein, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1ekm__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1ekm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ekm__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	32.92 Å
Rg (electron density)	32.21 Å
Total Rg	32.86 Å
Atom count	10396
Residues	1312
Excluded volume	184030 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ekm__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1ekm__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1ekm__assembly_3__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	COPPER AMINE OXIDASE
Molecular weight formula_weight	73731.1 kDa
EC 编号 ec_number	1.4.3.6
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	17070

APARPAHPLDPLSTAEIKAATNTVKSYFAGKKISFNTVTLREPARKAYIQWKEQGGPLPPRLAYYVILEAGKPGVKEGLVDLASLSVIETRALETVQPILTVEDLCSTEEVIRNDPAVIEQCVLSGIPANEMHKVYCDPWTIGYDERWGTGKRLQQALVYYRSDEDDSQYSHPLDFCPIVDTEEKKVIFIDIPNRRRKVSKHKHANFYPKHMIEKVGAMRPEAPPINVTQPEGVSFKMTGNVMEWSNFKFHIGFNYREGIVLSDVSYNDHGNVRPIFHRISLSEMIVPYGSPEFPHQRKHALDIGEYGAGYMTNPLSLGCDCKGVIHYLDAHFSDRAGDPITVKNAVCIHEEDDGLLFKHSDFRDNFATSLVTRATKLVVSQIFTAANYEYCLYWVFMQDGAIRLDIRLTGILNTYILGDDEEAGPWGTRVYPNVNAHNHQHLFSLRIDPRIDGDGNSAAACDAKSSPYPLGSPENMYGNAFYSEKTTFKTVKDSLTNYESATGRSWDIFNPNKVNPYSGKPPSYKLVSTQCPPLLAKEGSLVAKRAPWASHSVNVVPYKDNRLYPSGDHVPQWSGDGVRGMREWIGDGSENIDNTDILFFHTFGITHFPAPEDFPLMPAEPITLMLRPRHFFTENPGLDIQPSYAMTTSEAKRAV

Source Source

Source organism organism	Pichia angusta
NCBI taxonomy ID ncbi_taxonomy_id	4905
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1476

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d1ekma1
Class class	b — All beta proteins
Fold Fold fold	b.30 — Supersandwich
Superfamily Superfamily superfamily	b.30.2 — Amine oxidase catalytic domain
Family Family family	b.30.2.1 — Amine oxidase catalytic domain

Domain ID domain_id	d1ekma2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.2 — Amine oxidase N-terminal region
Family Family family	d.17.2.1 — Amine oxidase N-terminal region

Domain ID domain_id	d1ekma3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.2 — Amine oxidase N-terminal region
Family Family family	d.17.2.1 — Amine oxidase N-terminal region

Domain ID domain_id	d1ekmb1
Class class	b — All beta proteins
Fold Fold fold	b.30 — Supersandwich
Superfamily Superfamily superfamily	b.30.2 — Amine oxidase catalytic domain
Family Family family	b.30.2.1 — Amine oxidase catalytic domain

Domain ID domain_id	d1ekmb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.2 — Amine oxidase N-terminal region
Family Family family	d.17.2.1 — Amine oxidase N-terminal region

Domain ID domain_id	d1ekmb3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.2 — Amine oxidase N-terminal region
Family Family family	d.17.2.1 — Amine oxidase N-terminal region

Domain ID domain_id	d1ekmc1
Class class	b — All beta proteins
Fold Fold fold	b.30 — Supersandwich
Superfamily Superfamily superfamily	b.30.2 — Amine oxidase catalytic domain
Family Family family	b.30.2.1 — Amine oxidase catalytic domain

Domain ID domain_id	d1ekmc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.2 — Amine oxidase N-terminal region
Family Family family	d.17.2.1 — Amine oxidase N-terminal region

Domain ID domain_id	d1ekmc3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.2 — Amine oxidase N-terminal region
Family Family family	d.17.2.1 — Amine oxidase N-terminal region

CATH v4.4 (9 domains)

Domain ID domain_id	1ekmA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1ekmA02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1ekmA03
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	20 — Copper amine oxidase, catalytic domain

Domain ID domain_id	1ekmB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1ekmB02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1ekmB03
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	20 — Copper amine oxidase, catalytic domain

Domain ID domain_id	1ekmC01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1ekmC02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1ekmC03
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	20 — Copper amine oxidase, catalytic domain

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Unit-cell length a length_a	139.227 Å
Unit-cell length b length_b	153.515 Å
Unit-cell length c length_c	223.407 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	500.000 Å
R factor r_factor	0.1830
R_work r_work	0.1830
R_free r_free	0.2080

CRYSTAL STRUCTURE AT 2.5 A RESOLUTION OF ZINC-SUBSTITUTED COPPER AMINE OXIDASE OF HANSENULA POLYMORPHA EXPRESSED IN ESCHERICHIA COLI

1. Protein Identity and Related Structures Protein Identity & Related Structures

COPPER AMINE OXIDASE

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1ekm__assembly_1__model_1

1ekm__assembly_1__model_1 | I(q)

1ekm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

CATH v4.4 (9 domains)

7. Citations (2)

CRYSTAL STRUCTURE AT 2.5 A RESOLUTION OF ZINC-SUBSTITUTED COPPER AMINE OXIDASE OF HANSENULA POLYMORPHA EXPRESSED IN ESCHERICHIA COLI

1. Protein Identity and Related Structures Protein Identity & Related Structures

COPPER AMINE OXIDASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1ekm__assembly_1__model_1

1ekm__assembly_1__model_1 | I(q)

1ekm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

CATH v4.4 (9 domains)

7. Citations (2)