6r7d

Crystal structure of LTC4S in complex with AZ13690257

Method: X-RAY DIFFRACTION

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

Leukotriene C4 synthase

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	(1~{S},2~{S})-2-[5-[cyclopropylmethyl(naphthalen-1-yl)amino]-4-methoxy-pyrimidin-2-yl]carbonylcyclopropane-1-carboxylic acid × 3 NICKEL (II) ION × 3 PALMITIC ACID × 16 DODECYL-BETA-D-MALTOSIDE × 1 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	(1~{S},2~{S})-2-[5-[cyclopropylmethyl(naphthalen-1-yl)amino]-4-methoxy-pyrimidin-2-yl]carbonylcyclopropane-1-carboxylic acid × 3 NICKEL (II) ION × 1 PALMITIC ACID × 11 water × 3	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 3	(1~{S},2~{S})-2-[5-[cyclopropylmethyl(naphthalen-1-yl)amino]-4-methoxy-pyrimidin-2-yl]carbonylcyclopropane-1-carboxylic acid × 3 NICKEL (II) ION × 2 PALMITIC ACID × 7 water × 3	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 3	(1~{S},2~{S})-2-[5-[cyclopropylmethyl(naphthalen-1-yl)amino]-4-methoxy-pyrimidin-2-yl]carbonylcyclopropane-1-carboxylic acid × 3 NICKEL (II) ION × 2 PALMITIC ACID × 9 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LTC4S_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–157； UniProt 2–150 Author chain B； PDBConstruct 9–157； UniProt 2–150 Author chain C； PDBConstruct 9–157； UniProt 2–150 Author chain D； PDBConstruct 9–157； UniProt 2–150 Author chain E； PDBConstruct 9–157； UniProt 2–150 Author chain F； PDBConstruct 9–157； UniProt 2–150 Author chain G； PDBConstruct 9–157； UniProt 2–150 Author chain H； PDBConstruct 9–157； UniProt 2–150 Author chain I； PDBConstruct 9–157； UniProt 2–150 Author chain J； PDBConstruct 9–157； UniProt 2–150 Author chain K； PDBConstruct 9–157； UniProt 2–150 Author chain L； PDBConstruct 9–157； UniProt 2–150

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	6r7d
Deposition date deposition_date	2019-03-28
Structure title title	Crystal structure of LTC4S in complex with AZ13690257
Keywords keywords	Inhibitor, arachidonic acid cascade, cysteinyl leukotrienes, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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.

6r7d__assembly_1__model_1

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

Download this curve (.dat)

6r7d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6r7d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.24 Å
Rg (electron density)	22.89 Å
Total Rg	24.17 Å
Atom count	3853
Residues	446
Excluded volume	71385 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6r7d__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6r7d__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6r7d__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6r7d__assembly_4__model_1`	trimeric （3）	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	Leukotriene C4 synthase
Molecular weight formula_weight	17482.6 kDa
EC 编号 ec_number	4.4.1.20
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	15151

MAHHHHHHKDEVALLAAVTLLGVLLQAYFSLQVISARRAFRVSPPLTTGPPEFERVYRAQVNCSEYFPLFLATLWVAGIFFHEGAAALCGLVYLFARLRYFQGYARSAQLRLAPLYASARALWLLVALAALGLLAHFLPAALRAALLGRLRTLLPWA

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Komagataella pastoris

Entity 2 Entity 2 non-polymer

Description description	(1~{S},2~{S})-2-[5-[cyclopropylmethyl(naphthalen-1-yl)amino]-4-methoxy-pyrimidin-2-yl]carbonylcyclopropane-1-carboxylic acid
Molecular weight formula_weight	417.5 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	PALMITIC ACID
Molecular weight formula_weight	256.4 kDa
Source method src_method	syn
Copy count entity_count	43

Entity 5 Entity 5 non-polymer

Description description	DODECYL-BETA-D-MALTOSIDE
Molecular weight formula_weight	510.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	97

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	6r7dA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	550 — Membrane associated eicosanoid/glutathione metabolism-like domain

Domain ID domain_id	6r7dB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	550 — Membrane associated eicosanoid/glutathione metabolism-like domain

Domain ID domain_id	6r7dC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	550 — Membrane associated eicosanoid/glutathione metabolism-like domain

Domain ID domain_id	6r7dD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	550 — Membrane associated eicosanoid/glutathione metabolism-like domain

Domain ID domain_id	6r7dE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	550 — Membrane associated eicosanoid/glutathione metabolism-like domain

Domain ID domain_id	6r7dF00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	550 — Membrane associated eicosanoid/glutathione metabolism-like domain

Domain ID domain_id	6r7dG00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	550 — Membrane associated eicosanoid/glutathione metabolism-like domain

Domain ID domain_id	6r7dH00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	550 — Membrane associated eicosanoid/glutathione metabolism-like domain

Domain ID domain_id	6r7dI00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	550 — Membrane associated eicosanoid/glutathione metabolism-like domain

Domain ID domain_id	6r7dJ00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	550 — Membrane associated eicosanoid/glutathione metabolism-like domain

Domain ID domain_id	6r7dK00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	550 — Membrane associated eicosanoid/glutathione metabolism-like domain

Domain ID domain_id	6r7dL00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	550 — Membrane associated eicosanoid/glutathione metabolism-like domain

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Unit-cell length a length_a	121.591 Å
Unit-cell length b length_b	169.385 Å
Unit-cell length c length_c	174.478 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	48

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	121.534 Å
R factor r_factor	—
R_work r_work	0.2081
R_free r_free	0.2297

Crystal structure of LTC4S in complex with AZ13690257

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

Leukotriene C4 synthase

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

6r7d__assembly_1__model_1

6r7d__assembly_1__model_1 | I(q)

6r7d__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

Source Source

Entity 2 Entity 2 non-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) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of LTC4S in complex with AZ13690257

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

Leukotriene C4 synthase

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

6r7d__assembly_1__model_1

6r7d__assembly_1__model_1 | I(q)

6r7d__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

Source Source

Entity 2 Entity 2 non-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) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)