3nak

Crystal structure of the complex of goat lactoperoxidase with hypothiocyanite at 3.3 A resolution

Method: X-RAY DIFFRACTION

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

Lactoperoxidase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 4	alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 1-(OXIDOSULFANYL)METHANAMINE × 1 FORMIC ACID × 2 water × 1	Consistent with protein count
2	Other combination	Monomer	Protein 1 其他Polymer 4	alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 1-(OXIDOSULFANYL)METHANAMINE × 1 FORMIC ACID × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A3F9D6_CAPHI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–595； UniProt 118–712 Author chain B； PDBConstruct 1–595； UniProt 118–712

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	3nak
Deposition date deposition_date	2010-06-02
Structure title title	Crystal structure of the complex of goat lactoperoxidase with hypothiocyanite at 3.3 A resolution
Keywords keywords	LACTOPEROXIDASE, COMPLEX, HYPOTHIOCYANITE, FORMATE, MILK PROTEIN, METAL BINDING PROTEIN, 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.

3nak__assembly_1__model_1

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

Download this curve (.dat)

3nak__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3nak__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.18 Å
Rg (electron density)	23.93 Å
Total Rg	24.95 Å
Atom count	4956
Residues	594
Excluded volume	87909 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3nak__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3nak__assembly_2__model_1`	monomeric （1）	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 (9)

Entity 1 Entity 1 polymer

Description description	Lactoperoxidase
Molecular weight formula_weight	67609.8 kDa
EC 编号 ec_number	1.11.1.7
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	10098

SWEVGCGAPVPLVTCDEQSPYRTITGDCNNRRSPALGAANRALARWLPAEYEDGLAVPFGWTQRKTRNGFRVPLAREVSNKIVGYLDEEGVLDQNRSLLFMQWGQIVDHDLDFAPETELGSSEHSKVQCEEYCVQGDECFPIMFPKNDPKLKTQGKCMPFFRAGFVCPTPPYQSLARDQINAVTSFLDASLVYGSEPSLASRLRNLSSPLGLMAVNQEAWDHGLAYPPFNNVKPSPCEFINTTAHVPCFQAGDSRASEQILLATVHTLLLREHNRLARELKRLNPHWDGEMLYQEARKILGAFIQIITFRDYLPIVLGSEMQKWIPPYQGYNNSVDPRISNVFTFAFRFGHMEVPSTVSRLDENYQPWGPEAELPLHTLFFNTWRIIKDGGIDPLVRGLLAKNSKLMNQNKMVTSELRNKLFQPTHKVHGFDLAAINLQRCRDHGMPGYNSWRGFCGLSQPKTLKGLQAVLKNKVLAKKLLDLYKTPDNIDIWIGGNAEPMVERGRVGPLLACLLGRQFQQIRDGDRFWWENPGVFTEKQRDSLQKVSFSRLICDNTHITKVPLHAFQANNYPHDFVDCSAVDKLDLSPWASREN

Entity 2 Entity 2 branched

Description description	alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	3

Entity 3 Entity 3 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	3

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	1-(OXIDOSULFANYL)METHANAMINE
Molecular weight formula_weight	79.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	186

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3nakA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	640 — Myeloperoxidase, subunit C
Homologous superfamily homologous superfamily	10 — Haem peroxidase domain superfamily, animal type

Domain ID domain_id	3nakB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	640 — Myeloperoxidase, subunit C
Homologous superfamily homologous superfamily	10 — Haem peroxidase domain superfamily, animal type

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Unit-cell length a length_a	57.991 Å
Unit-cell length b length_b	72.272 Å
Unit-cell length c length_c	83.652 Å
Unit-cell angle α angle_alpha	85.45 °
Unit-cell angle β angle_beta	84.04 °
Unit-cell angle γ angle_gamma	75.89 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	19.870 Å
R factor r_factor	0.2077
R_work r_work	0.2047
R_free r_free	0.2430

Crystal structure of the complex of goat lactoperoxidase with hypothiocyanite at 3.3 A resolution

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

Lactoperoxidase

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

3nak__assembly_1__model_1

3nak__assembly_1__model_1 | I(q)

3nak__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the complex of goat lactoperoxidase with hypothiocyanite at 3.3 A resolution

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

Lactoperoxidase

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

3nak__assembly_1__model_1

3nak__assembly_1__model_1 | I(q)

3nak__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)