4dl1

Crystal Structure of human Myeloperoxidase with covalent thioxanthine analog

Method: X-RAY DIFFRACTION

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

Myeloperoxidase light chain

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 4 其他Polymer 2	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 CHLORIDE ION × 2 3-[(2R)-2-ethoxypropyl]-2-thioxo-1,2,3,9-tetrahydro-6H-purin-6-one × 2 PROTOPORPHYRIN IX CONTAINING FE × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CALCIUM ION × 2 water × 4	Consistent with protein count
10	Other combination	Homooligomer	Protein 2 其他Polymer 1	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 CHLORIDE ION × 1 3-[(2R)-2-ethoxypropyl]-2-thioxo-1,2,3,9-tetrahydro-6H-purin-6-one × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CALCIUM ION × 1 water × 2	Consistent with protein count
11	Other combination	Homooligomer	Protein 2 其他Polymer 1	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 CHLORIDE ION × 1 3-[(2R)-2-ethoxypropyl]-2-thioxo-1,2,3,9-tetrahydro-6H-purin-6-one × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CALCIUM ION × 1 water × 2	Consistent with protein count
12	Other combination	Homooligomer	Protein 2 其他Polymer 2	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 CHLORIDE ION × 1 3-[(2R)-2-ethoxypropyl]-2-thioxo-1,2,3,9-tetrahydro-6H-purin-6-one × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 1 water × 2	Consistent with protein count
2	Other combination	Homooligomer	Protein 4 其他Polymer 2	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 CHLORIDE ION × 2 3-[(2R)-2-ethoxypropyl]-2-thioxo-1,2,3,9-tetrahydro-6H-purin-6-one × 2 PROTOPORPHYRIN IX CONTAINING FE × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CALCIUM ION × 2 water × 4	Consistent with protein count
3	Other combination	Homooligomer	Protein 4 其他Polymer 2	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 CHLORIDE ION × 2 3-[(2R)-2-ethoxypropyl]-2-thioxo-1,2,3,9-tetrahydro-6H-purin-6-one × 2 PROTOPORPHYRIN IX CONTAINING FE × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CALCIUM ION × 2 water × 4	Consistent with protein count
4	Other combination	Homooligomer	Protein 4 其他Polymer 3	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 CHLORIDE ION × 2 3-[(2R)-2-ethoxypropyl]-2-thioxo-1,2,3,9-tetrahydro-6H-purin-6-one × 2 PROTOPORPHYRIN IX CONTAINING FE × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CALCIUM ION × 2 water × 4	Consistent with protein count
5	Other combination	Homooligomer	Protein 2 其他Polymer 1	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 CHLORIDE ION × 1 3-[(2R)-2-ethoxypropyl]-2-thioxo-1,2,3,9-tetrahydro-6H-purin-6-one × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CALCIUM ION × 1 water × 2	Consistent with protein count
6	Other combination	Homooligomer	Protein 2 其他Polymer 1	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 CHLORIDE ION × 1 3-[(2R)-2-ethoxypropyl]-2-thioxo-1,2,3,9-tetrahydro-6H-purin-6-one × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CALCIUM ION × 1 water × 2	Consistent with protein count
7	Other combination	Homooligomer	Protein 2 其他Polymer 1	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 CHLORIDE ION × 1 3-[(2R)-2-ethoxypropyl]-2-thioxo-1,2,3,9-tetrahydro-6H-purin-6-one × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CALCIUM ION × 1 water × 2	Consistent with protein count
8	Other combination	Homooligomer	Protein 2 其他Polymer 1	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 CHLORIDE ION × 1 3-[(2R)-2-ethoxypropyl]-2-thioxo-1,2,3,9-tetrahydro-6H-purin-6-one × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CALCIUM ION × 1 water × 2	Consistent with protein count
9	Other combination	Homooligomer	Protein 2 其他Polymer 1	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 CHLORIDE ION × 1 3-[(2R)-2-ethoxypropyl]-2-thioxo-1,2,3,9-tetrahydro-6H-purin-6-one × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CALCIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PERM_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–104； UniProt 167–270 Author chain B； PDBConstruct 1–104； UniProt 167–270 Author chain E； PDBConstruct 1–104； UniProt 167–270 Author chain F； PDBConstruct 1–104； UniProt 167–270 Author chain I； PDBConstruct 1–104； UniProt 167–270 Author chain J； PDBConstruct 1–104； UniProt 167–270 Author chain M； PDBConstruct 1–104； UniProt 167–270 Author chain N； PDBConstruct 1–104； UniProt 167–270 Author chain C； PDBConstruct 1–466； UniProt 279–744 Author chain D； PDBConstruct 1–466； UniProt 279–744 Author chain G； PDBConstruct 1–466； UniProt 279–744 Author chain H； PDBConstruct 1–466； UniProt 279–744 Author chain K； PDBConstruct 1–466； UniProt 279–744 Author chain L； PDBConstruct 1–466； UniProt 279–744 Author chain O； PDBConstruct 1–466； UniProt 279–744 Author chain P； PDBConstruct 1–466； UniProt 279–744

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	4dl1
Deposition date deposition_date	2012-02-05
Structure title title	Crystal Structure of human Myeloperoxidase with covalent thioxanthine analog
Keywords keywords	oxidoreductase, Heme-dependent peroxidase; 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.

4dl1__assembly_1__model_1

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

Download this curve (.dat)

4dl1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4dl1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.03 Å
Rg (electron density)	33.47 Å
Total Rg	34.02 Å
Atom count	9450
Residues	1137
Excluded volume	167640 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4dl1__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4dl1__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4dl1__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4dl1__assembly_4__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`4dl1__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`4dl1__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`4dl1__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`4dl1__assembly_8__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`4dl1__assembly_9__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`4dl1__assembly_10__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`4dl1__assembly_11__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
12	1	`4dl1__assembly_12__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 (10)

Entity 1 Entity 1 polymer

Description description	Myeloperoxidase light chain
Molecular weight formula_weight	11903.3 kDa
EC 编号 ec_number	1.11.2.2
Source method src_method	nat
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,E,F,I,J,M,N
Atom count atom_count	40392

CPEQDKYRTITGMCNNRRSPTLGASNRAFVRWLPAEYEDGFSLPYGWTPGVKRNGFPVALARAVSNEIVRFPTDQLTPDQERSLMFMQWGQLLDHDLDFTPEPA

Entity 2 Entity 2 polymer

Description description	Myeloperoxidase heavy chain
Molecular weight formula_weight	53234.2 kDa
EC 编号 ec_number	1.11.2.2
Source method src_method	nat
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,G,H,K,L,O,P

VNCETSCVQQPPCFPLKIPPNDPRIKNQADCIPFFRSCPACPGSNITIRNQINALTSFVDASMVYGSEEPLARNLRNMSNQLGLLAVNQRFQDNGRALLPFDNLHDDPCLLTNRSARIPCFLAGDTRSSEMPELTSMHTLLLREHNRLATELKSLNPRWDGERLYQEARKIVGAMVQIITYRDYLPLVLGPTAMRKYLPTYRSYNDSVDPRIANVFTNAFRYGHTLIQPFMFRLDNRYQPMEPNPRVPLSRVFFASWRVVLEGGIDPILRGLMATPAKLNRQNQIAVDEIRERLFEQVMRIGLDLPALNMQRSRDHGLPGYNAWRRFCGLPQPETVGQLGTVLRNLKLARKLMEQYGTPNNIDIWMGGVSEPLKRKGRVGPLLACIIGTQFRKLRDGDRFWWENEGVFSMQQRQALAQISLPRIICDNTGITTVSKNNIFMSNSYPRDFVNCSTLPALNLASWREA

Entity 3 Entity 3 branched

Description description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1057.0 kDa
Source method src_method	man
Copy count entity_count	8

Entity 4 Entity 4 branched

Description description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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	910.8 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 6 Entity 6 non-polymer

Description description	3-[(2R)-2-ethoxypropyl]-2-thioxo-1,2,3,9-tetrahydro-6H-purin-6-one
Molecular weight formula_weight	254.3 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 7 Entity 7 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 8 Entity 8 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	15

Entity 9 Entity 9 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2520

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	4dl1C00
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	4dl1D00
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	4dl1G00
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	4dl1H00
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	4dl1K00
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	4dl1L00
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	4dl1O00
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	4dl1P00
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	63.829 Å
Unit-cell length b length_b	242.636 Å
Unit-cell length c length_c	151.505 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.19 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	128.490 Å
R factor r_factor	0.1933
R_work r_work	0.1905
R_free r_free	0.2462

Crystal Structure of human Myeloperoxidase with covalent thioxanthine analog

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

Myeloperoxidase light chain

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

4dl1__assembly_1__model_1

4dl1__assembly_1__model_1 | I(q)

4dl1__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

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 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal Structure of human Myeloperoxidase with covalent thioxanthine analog

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

Myeloperoxidase light chain

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

4dl1__assembly_1__model_1

4dl1__assembly_1__model_1 | I(q)

4dl1__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

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 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)