5ff1

Two way mode of binding of antithyroid drug methimazole to mammalian heme peroxidases: Structure of the complex of lactoperoxidase with methimazole at 1.97 Angstrom 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	Protein monomer	Monomer	Protein 1	1-METHYL-1,3-DIHYDRO-2H-IMIDAZOLE-2-THIONE × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 PROTOPORPHYRIN IX CONTAINING FE × 1 CALCIUM ION × 1 NITRATE ION × 5 GLYCEROL × 4 water × 1	Consistent with protein count
2	Other combination	Monomer	Protein 1 其他Polymer 1	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 1-METHYL-1,3-DIHYDRO-2H-IMIDAZOLE-2-THIONE × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PROTOPORPHYRIN IX CONTAINING FE × 1 CALCIUM ION × 1 NITRATE ION × 4 GLYCEROL × 4 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	5ff1
Deposition date deposition_date	2015-12-17
Structure title title	Two way mode of binding of antithyroid drug methimazole to mammalian heme peroxidases: Structure of the complex of lactoperoxidase with methimazole at 1.97 Angstrom resolution
Keywords keywords	Inhibitor, peroxidase, 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.

5ff1__assembly_1__model_1

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

Download this curve (.dat)

5ff1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ff1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.85 Å
Rg (electron density)	23.65 Å
Total Rg	24.59 Å
Atom count	4912
Residues	595
Excluded volume	86969 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ff1__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5ff1__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	67529.8 kDa
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	10608

SWEVGCGAPVPLVTCDEQSPYRTITGDCNNRRSPALGAANRALARWLPAEYEDGLAVPFGWTQRKTRNGFRVPLAREVSNKIVGYLDEEGVLDQNRSLLFMQWGQIVDHDLDFAPETELGSSEHSKVQCEEYCVQGDECFPIMFPKNDPKLKTQGKCMPFFRAGFVCPTPPYQSLARDQINAVTSFLDASLVYGSEPSLASRLRNLSSPLGLMAVNQEAWDHGLAYPPFNNVKPSPCEFINTTAHVPCFQAGDSRASEQILLATVHTLLLREHNRLARELKRLNPHWDGEMLYQEARKILGAFIQIITFRDYLPIVLGSEMQKWIPPYQGYNNSVDPRISNVFTFAFRFGHMEVPSTVSRLDENYQPWGPEAELPLHTLFFNTWRIIKDGGIDPLVRGLLAKNSKLMNQNKMVTSELRNKLFQPTHKVHGFDLAAINLQRCRDHGMPGYNSWRGFCGLSQPKTLKGLQAVLKNKVLAKKLLDLYKTPDNIDIWIGGNAEPMVERGRVGPLLACLLGRQFQQIRDGDRFWWENPGVFTEKQRDSLQKVSFSRLICDNTHITKVPLHAFQANNYPHDFVDCSAVDKLDLSPWASREN

Entity 2 Entity 2 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	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	1-METHYL-1,3-DIHYDRO-2H-IMIDAZOLE-2-THIONE
Molecular weight formula_weight	114.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 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 6 Entity 6 non-polymer

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

Entity 7 Entity 7 non-polymer

Description description	NITRATE ION
Molecular weight formula_weight	62.0 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 8 Entity 8 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	775

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5ff1A00
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	5ff1B00
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	80.310 Å
Unit-cell length b length_b	93.020 Å
Unit-cell length c length_c	81.530 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	89.97 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.970 Å
Low-resolution limit resolution_low	40.430 Å
R factor r_factor	0.1782
R_work r_work	0.1767
R_free r_free	0.2259

Two way mode of binding of antithyroid drug methimazole to mammalian heme peroxidases: Structure of the complex of lactoperoxidase with methimazole at 1.97 Angstrom 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

5ff1__assembly_1__model_1

5ff1__assembly_1__model_1 | I(q)

5ff1__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 non-polymer

Entity 4 Entity 4 non-polymer

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)

Two way mode of binding of antithyroid drug methimazole to mammalian heme peroxidases: Structure of the complex of lactoperoxidase with methimazole at 1.97 Angstrom 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

5ff1__assembly_1__model_1

5ff1__assembly_1__model_1 | I(q)

5ff1__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 non-polymer

Entity 4 Entity 4 non-polymer

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)