SAXSdb — 3zdn

▼

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

MONOAMINE OXIDASE N

ASPERGILLUS NIGER

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	1,2-ETHANEDIOL × 2 FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	1,2-ETHANEDIOL × 2 FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AOFN_ASPNG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–495； UniProt 1–495 Author chain B； PDBConstruct 1–495； UniProt 1–495 Author chain C； PDBConstruct 1–495； UniProt 1–495 Author chain D； PDBConstruct 1–495； UniProt 1–495

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3zdn
Deposition date deposition_date	2012-11-29
Structure title title	D11-C mutant of monoamine oxidase from Aspergillus niger
Keywords keywords	OXIDOREDUCTASE, FLAVIN DEPENDENT OXIDASE, AMINES; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3zdn__assembly_1__model_1

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

Download this curve (.dat)

3zdn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3zdn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.10 Å
Rg (electron density)	28.28 Å
Total Rg	29.15 Å
Atom count	7534
Residues	955
Excluded volume	132140 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3zdn__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3zdn__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	MONOAMINE OXIDASE N
Molecular weight formula_weight	55367.1 kDa
EC 编号 ec_number	1.4.3.4
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	15560

MTSRDGYQWTPETGLTQGVPSLGVISPPTNIEDTDKDGPWDVIVIGGGYCGLTATRDLTVAGFKTLLLEARDRIGGRSWSSNIDGYPYEMGGTWVHWHQSHVWREITRYKMHNALSPSFNFSRGVNHFQLRTNPTTSTYMTHEAEDELLRSALHKFTNVDGTNGRTVLPFPHDMFYVPEFRKYDEMSYSERIDQIRDELSLNERSSLEALILTCSGGTLENSSFGEFLHWWAMSGYTYQGCQDCLTSYKFKDGQSAFARRFWEEAAGTGRLGYVFGCPVRSVVNERDAARVTARDGREFVAKRVVCTIPLNVLSTIQFSPALSTERISAMQAGHVSMCTKVHAEVDNKDMRSWTGIAYPFNKLCYAIGDGTTPAGNTHLVCFGNSANHIQPDEDVRETLKAVGQLAPGTFGVKRLVFHNWVKDEFAKGAGFFSRPGMVSECLQGLREKHGGVVFANSDWALGWRSFIDGAIEEGTRAARVVLEELGTKREVKARL

Source Source

Source organism organism	ASPERGILLUS NIGER
NCBI taxonomy ID ncbi_taxonomy_id	5061
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	539

▼

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	3zdnA01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	3zdnA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	660 — Polyamine Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3zdnB01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	3zdnB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	660 — Polyamine Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3zdnC01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	3zdnC02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	660 — Polyamine Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3zdnD01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	3zdnD02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	660 — Polyamine Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

▶

Unit-cell length a length_a	108.600 Å
Unit-cell length b length_b	119.340 Å
Unit-cell length c length_c	178.780 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	99.260 Å
R factor r_factor	0.1558
R_work r_work	0.1527
R_free r_free	0.2143

D11-C mutant of monoamine oxidase from Aspergillus niger

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

MONOAMINE OXIDASE N

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

3zdn__assembly_1__model_1

3zdn__assembly_1__model_1 | I(q)

3zdn__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

D11-C mutant of monoamine oxidase from Aspergillus niger

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

MONOAMINE OXIDASE N

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

3zdn__assembly_1__model_1

3zdn__assembly_1__model_1 | I(q)

3zdn__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)