1e0y

Structure of the D170S/T457E double mutant of vanillyl-alcohol oxidase

Method: X-RAY DIFFRACTION

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

VANILLYL-ALCOHOL OXIDASE

PENICILLIUM SIMPLICISSIMUM

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VAOX_PENSI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–560； UniProt 1–560 Author chain B； PDBConstruct 1–560； UniProt 1–560

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	1e0y
Deposition date deposition_date	2000-04-11
Structure title title	Structure of the D170S/T457E double mutant of vanillyl-alcohol oxidase
Keywords keywords	FLAVOENZYME, SPECIFICITY; FLAVOENZYME
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.

1e0y__assembly_1__model_1

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

Download this curve (.dat)

1e0y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1e0y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.28 Å
Rg (electron density)	29.38 Å
Total Rg	30.11 Å
Atom count	8673
Residues	1100
Excluded volume	154070 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1e0y__assembly_1__model_1`	dimeric （2）	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 (4)

Entity 1 Entity 1 polymer

Description description	VANILLYL-ALCOHOL OXIDASE
Molecular weight formula_weight	63007.0 kDa
EC 编号 ec_number	1.1.3.38
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8753

MSKTQEFRPLTLPPKLSLSDFNEFIQDIIRIVGSENVEVISSKDQIVDGSYMKPTHTHDPHHVMDQDYFLASAIVAPRNVADVQSIVGLANKFSFPLWPISIGRNSGYGGAAPRVSGSVVLDMGKNMNRVLEVNVEGAYCVVEPGVTYHDLHNYLEANNLRDKLWLDVPSLGGGSVLGNAVERGVGYTPYGDHWMMHSGMEVVLANGELLRTGMGALPDPKRPETMGLKPEDQPWSKIAHLFPYGFGPYIDGLFSQSNMGIVTKIGIWLMPNPGGYQSYLITLPKDGDLKQAVDIIRPLRLGMALQNVPTIRHILLDAAVLGDKRSYSSRTEPLSDEELDKIAKQLNLGRWNFYGALYGPEPIRRVLWETIKDAFSAIPGVKFYFPEDTPENSVLRVRDKTMQGIPTYDELKWIDWLPNGAHLFFSPIAKVSGEDAMMQYAVTKKRCQEAGLDFIGEFTVGMREMHHIVCIVFNKKDLIQKRKVQWLMRTLIDDCAANGWGEYRTHLAFMDQIMETYNWNNSSFLRFNEVLKNAVDPNGIIAPGKSGVWPSQYSHVTWKL

Source Source

Source organism organism	PENICILLIUM SIMPLICISSIMUM
NCBI taxonomy ID ncbi_taxonomy_id	69488
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ALPHA,ALPHA,ALPHA-TRIFLUORO-P-CRESOL
Molecular weight formula_weight	162.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	80

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1e0ya1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.32 — FAD-linked oxidases, C-terminal domain
Family Family family	d.58.32.1 — Vanillyl-alcohol oxidase-like

Domain ID domain_id	d1e0ya2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.145 — FAD-binding/transporter-associated domain-like
Superfamily Superfamily superfamily	d.145.1 — FAD-binding/transporter-associated domain-like
Family Family family	d.145.1.1 — FAD-linked oxidases, N-terminal domain

Domain ID domain_id	d1e0yb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.32 — FAD-linked oxidases, C-terminal domain
Family Family family	d.58.32.1 — Vanillyl-alcohol oxidase-like

Domain ID domain_id	d1e0yb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.145 — FAD-binding/transporter-associated domain-like
Superfamily Superfamily superfamily	d.145.1 — FAD-binding/transporter-associated domain-like
Family Family family	d.145.1.1 — FAD-linked oxidases, N-terminal domain

CATH v4.4 (8 domains)

Domain ID domain_id	1e0yA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2

Domain ID domain_id	1e0yA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1e0yA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	462 — Vanillyl-alcohol Oxidase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — FAD-linked oxidases, C-terminal domain

Domain ID domain_id	1e0yA04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	45 — Vanillyl-alcohol Oxidase; Chain A, domain 4
Homologous superfamily homologous superfamily	10 — Vanillyl-alcohol Oxidase; Chain A, domain 4

Domain ID domain_id	1e0yB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2

Domain ID domain_id	1e0yB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1e0yB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	462 — Vanillyl-alcohol Oxidase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — FAD-linked oxidases, C-terminal domain

Domain ID domain_id	1e0yB04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	45 — Vanillyl-alcohol Oxidase; Chain A, domain 4
Homologous superfamily homologous superfamily	10 — Vanillyl-alcohol Oxidase; Chain A, domain 4

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Unit-cell length a length_a	131.281 Å
Unit-cell length b length_b	131.281 Å
Unit-cell length c length_c	134.355 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	I 4
Space-group number int_tables_number	79
Crystal system crystal_system	—

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2250
R_work r_work	0.2250
R_free r_free	0.2870

Structure of the D170S/T457E double mutant of vanillyl-alcohol oxidase

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

VANILLYL-ALCOHOL 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

1e0y__assembly_1__model_1

1e0y__assembly_1__model_1 | I(q)

1e0y__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) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Structure of the D170S/T457E double mutant of vanillyl-alcohol oxidase

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

VANILLYL-ALCOHOL 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

1e0y__assembly_1__model_1

1e0y__assembly_1__model_1 | I(q)

1e0y__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) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)