SAXSdb — 2y9x

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

POLYPHENOL OXIDASE

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	LECTIN-LIKE FOLD PROTEIN × 1 COPPER (II) ION × 2 HOLMIUM ATOM × 1 2-HYDROXYCYCLOHEPTA-2,4,6-TRIEN-1-ONE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	LECTIN-LIKE FOLD PROTEIN × 1 COPPER (II) ION × 2 HOLMIUM ATOM × 1 2-HYDROXYCYCLOHEPTA-2,4,6-TRIEN-1-ONE × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	LECTIN-LIKE FOLD PROTEIN × 1 COPPER (II) ION × 2 HOLMIUM ATOM × 1 2-HYDROXYCYCLOHEPTA-2,4,6-TRIEN-1-ONE × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	LECTIN-LIKE FOLD PROTEIN × 1 COPPER (II) ION × 2 HOLMIUM ATOM × 1 2-HYDROXYCYCLOHEPTA-2,4,6-TRIEN-1-ONE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C7FF04_AGABI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–391； UniProt 2–392 Author chain B； PDBConstruct 1–391； UniProt 2–392 Author chain C； PDBConstruct 1–391； UniProt 2–392 Author chain D； PDBConstruct 1–391； UniProt 2–392

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	2y9x
Deposition date deposition_date	2011-02-17
Structure title title	Crystal structure of PPO3, a tyrosinase from Agaricus bisporus, in deoxy-form that contains additional unknown lectin-like subunit, with inhibitor tropolone
Keywords keywords	OXIDOREDUCTASE, COPPER-CONTAINING, PIGMENTATION, TYPE-3 COPPER PROTEIN; 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.

2y9x__assembly_1__model_1

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

Download this curve (.dat)

2y9x__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2y9x__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.07 Å
Rg (electron density)	25.19 Å
Total Rg	26.02 Å
Atom count	4275
Residues	527
Excluded volume	75380 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2y9x__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2y9x__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2y9x__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2y9x__assembly_4__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 (6)

Entity 1 Entity 1 polymer

Description description	POLYPHENOL OXIDASE
Molecular weight formula_weight	45318.6 kDa
EC 编号 ec_number	1.14.18.1
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	17125

SDKKSLMPLVGIPGEIKNRLNILDFVKNDKFFTLYVRALQVLQARDQSDYSSFFQLGGIHGLPYTEWAKAQPQLHLYKANYCTHGTVLFPTWHRAYESTWEQTLWEAAGTVAQRFTTSDQAEWIQAAKDLRQPFWDWGYWPNDPDFIGLPDQVIRDKQVEITDYNGTKIEVENPILHYKFHPIEPTFEGDFAQWQTTMRYPDVQKQENIEGMIAGIKAAAPGFREWTFNMLTKNYTWELFSNHGAVVGAHANSLEMVHNTVHFLIGRDPTLDPLVPGHMGSVPHAAFDPIFWMHHCNVDRLLALWQTMNYDVYVSEGMNREATMGLIPGQVLTEDSPLEPFYTKNQDPWQSDDLEDWETLGFSYPDFDPVKGKSKEEKSVYINDWVHKHYG

Entity 2 Entity 2 polymer

Description description	LECTIN-LIKE FOLD PROTEIN
Molecular weight formula_weight	16478.3 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

MAQARKIPLDLPGTRILNGANWANNSATENLATNSGTLIIFDQSTPGQDADRWLIHNYLDGYKIFNMGSNNWASVSRGNTVLGVSEFDGQTCKWSIEYSGNGEEFWIRVPREGGGGAVWTIKPASSQGPTTVFLDLLKETDPNQRIKFAV

Entity 3 Entity 3 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	HOLMIUM ATOM
Molecular weight formula_weight	164.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	2-HYDROXYCYCLOHEPTA-2,4,6-TRIEN-1-ONE
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	25

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	2y9xA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1280 — di-copper center containing domain from catechol oxidase
Homologous superfamily homologous superfamily	10 — Di-copper center containing domain from catechol oxidase

Domain ID domain_id	2y9xB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1280 — di-copper center containing domain from catechol oxidase
Homologous superfamily homologous superfamily	10 — Di-copper center containing domain from catechol oxidase

Domain ID domain_id	2y9xC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1280 — di-copper center containing domain from catechol oxidase
Homologous superfamily homologous superfamily	10 — Di-copper center containing domain from catechol oxidase

Domain ID domain_id	2y9xD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1280 — di-copper center containing domain from catechol oxidase
Homologous superfamily homologous superfamily	10 — Di-copper center containing domain from catechol oxidase

Domain ID domain_id	2y9xE00
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2y9xF00
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2y9xG00
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2y9xH00
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

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Unit-cell length a length_a	103.840 Å
Unit-cell length b length_b	104.820 Å
Unit-cell length c length_c	119.360 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.45 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.780 Å
Low-resolution limit resolution_low	58.030 Å
R factor r_factor	0.2380
R_work r_work	0.2350
R_free r_free	0.2890

Crystal structure of PPO3, a tyrosinase from Agaricus bisporus, in deoxy-form that contains additional unknown lectin-like subunit, with inhibitor tropolone

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

POLYPHENOL 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

2y9x__assembly_1__model_1

2y9x__assembly_1__model_1 | I(q)

2y9x__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of PPO3, a tyrosinase from Agaricus bisporus, in deoxy-form that contains additional unknown lectin-like subunit, with inhibitor tropolone

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

POLYPHENOL 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

2y9x__assembly_1__model_1

2y9x__assembly_1__model_1 | I(q)

2y9x__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)