6wyd

CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-12 (AKA; 7-benzyl-1H-[1,2,3]triazolo[4,5-b]pyrid

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	Protein homooligomer	Homooligomer	Protein 2	CHLORIDE ION × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 alpha-L-fucopyranose × 1 HEME C × 1 beta-D-mannopyranose × 1 alpha-D-mannopyranose × 2 7-benzyl-1H-[1,2,3]triazolo[4,5-b]pyridin-5-amine × 1 CALCIUM ION × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	CHLORIDE ION × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 alpha-L-fucopyranose × 1 HEME C × 1 beta-D-mannopyranose × 1 alpha-D-mannopyranose × 2 7-benzyl-1H-[1,2,3]triazolo[4,5-b]pyridin-5-amine × 1 CALCIUM ION × 1 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	CHLORIDE ION × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 alpha-L-fucopyranose × 1 HEME C × 1 beta-D-mannopyranose × 1 alpha-D-mannopyranose × 2 7-benzyl-1H-[1,2,3]triazolo[4,5-b]pyridin-5-amine × 1 CALCIUM ION × 1 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	CHLORIDE ION × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 alpha-L-fucopyranose × 1 HEME C × 1 beta-D-mannopyranose × 1 alpha-D-mannopyranose × 2 7-benzyl-1H-[1,2,3]triazolo[4,5-b]pyridin-5-amine × 1 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 1–105； UniProt 167–271 Author chain D； PDBConstruct 1–105； UniProt 167–271 Author chain F； PDBConstruct 1–105； UniProt 167–271 Author chain H； PDBConstruct 1–105； UniProt 167–271 Author chain B； PDBConstruct 1–467； UniProt 279–745 Author chain E； PDBConstruct 1–467； UniProt 279–745 Author chain G； PDBConstruct 1–467； UniProt 279–745 Author chain I； PDBConstruct 1–467； UniProt 279–745

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	6wyd
Deposition date deposition_date	2020-05-12
Structure title title	CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-12 (AKA; 7-benzyl-1H-[1,2,3]triazolo[4,5-b]pyrid
Keywords keywords	MYELOPEROXIDASE, 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.

6wyd__assembly_1__model_1

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

Download this curve (.dat)

6wyd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6wyd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.25 Å
Rg (electron density)	22.97 Å
Total Rg	23.93 Å
Atom count	4628
Residues	568
Excluded volume	82320 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6wyd__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6wyd__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6wyd__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6wyd__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 (11)

Entity 1 Entity 1 polymer

Description description	Myeloperoxidase light chain
Molecular weight formula_weight	11974.4 kDa
EC 编号 ec_number	1.11.2.2
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,F,H
Atom count atom_count	18734

CPEQDKYRTITGMCNNRRSPTLGASNRAFVRWLPAEYEDGFSLPYGWTPGVKRNGFPVALARAVSNEIVRFPTDQLTPDQERSLMFMQWGQLLDHDLDFTPEPAA

Entity 2 Entity 2 polymer

Description description	Myeloperoxidase heavy chain
Molecular weight formula_weight	53305.3 kDa
EC 编号 ec_number	1.11.2.2
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E,G,I

VNCETSCVQQPPCFPLKIPPNDPRIKNQADCIPFFRSCPACPGSNITIRNQINALTSFVDASMVYGSEEPLARNLRNMSNQLGLLAVNQRFQDNGRALLPFDNLHDDPCLLTNRSARIPCFLAGDTRSSEMPELTSMHTLLLREHNRLATELKSLNPRWDGERLYQEARKIVGAMVQIITYRDYLPLVLGPTAMRKYLPTYRSYNDSVDPRIANVFTNAFRYGHTLIQPFMFRLDNRYQPMEPNPRVPLSRVFFASWRVVLEGGIDPILRGLMATPAKLNRQNQIAVDEIRERLFEQVMRIGLDLPALNMQRSRDHGLPGYNAWRRFCGLPQPETVGQLGTVLRNLKLARKLMEQYGTPNNIDIWMGGVSEPLKRKGRVGPLLACIIGTQFRKLRDGDRFWWENEGVFSMQQRQALAQISLPRIICDNTGITTVSKNNIFMSNSYPRDFVNCSTLPALNLASWREAS

Entity 3 Entity 3 non-polymer

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

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	man
Copy count entity_count	19

Entity 5 Entity 5 non-polymer

Description description	alpha-L-fucopyranose
Molecular weight formula_weight	164.2 kDa
Source method src_method	man
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	beta-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	alpha-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	8

Entity 9 Entity 9 non-polymer

Description description	7-benzyl-1H-[1,2,3]triazolo[4,5-b]pyridin-5-amine
Molecular weight formula_weight	225.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 10 Entity 10 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	260

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Unit-cell length a length_a	143.683 Å
Unit-cell length b length_b	150.651 Å
Unit-cell length c length_c	231.060 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	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	115.530 Å
R factor r_factor	0.1965
R_work r_work	0.1935
R_free r_free	0.2539

CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-12 (AKA; 7-benzyl-1H-[1,2,3]triazolo[4,5-b]pyrid

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

6wyd__assembly_1__model_1

6wyd__assembly_1__model_1 | I(q)

6wyd__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 (11)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 water

7. Citations (1)

CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-12 (AKA; 7-benzyl-1H-[1,2,3]triazolo[4,5-b]pyrid

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

6wyd__assembly_1__model_1

6wyd__assembly_1__model_1 | I(q)

6wyd__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 (11)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 water

7. Citations (1)