SAXSdb — 5j6d

▼

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

Tryptophan 5-hydroxylase 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	FE (III) ION × 1 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GLYCEROL × 1 4-[(N-{[2-(3-methoxyphenoxy)-6-(piperidin-1-yl)phenyl]methyl}carbamimidoyl)carbamoyl]-L-phenylalanine × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	FE (III) ION × 1 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GLYCEROL × 1 4-[(N-{[2-(3-methoxyphenoxy)-6-(piperidin-1-yl)phenyl]methyl}carbamimidoyl)carbamoyl]-L-phenylalanine × 1 water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	FE (III) ION × 2 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 GLYCEROL × 2 4-[(N-{[2-(3-methoxyphenoxy)-6-(piperidin-1-yl)phenyl]methyl}carbamimidoyl)carbamoyl]-L-phenylalanine × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TPH1_HUMAN
Isoform	P17752-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–301； UniProt 102–402 Author chain B； PDBConstruct 1–301； UniProt 102–402

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5j6d
Deposition date deposition_date	2016-04-04
Structure title title	Discovery of acyl guanidine tryptophan hydroxylase-1 inhibitors
Keywords keywords	TPH1, Iron, acyl, quanidine, OXIDOREDUCTASE-INHIBITOR complex; OXIDOREDUCTASE/INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

▼

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.

5j6d__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5j6d__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5j6d__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	18.16 Å
Rg (electron density)	16.92 Å
Total Rg	17.99 Å
Atom count	1818
Residues	248
Excluded volume	32050 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5j6d__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5j6d__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5j6d__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Tryptophan 5-hydroxylase 1
Molecular weight formula_weight	35455.3 kDa
EC 编号 ec_number	1.14.16.4
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4335

METVPWFPKKISDLDHCANRVLMYGSELDADHPGFKDNVYRKRRKYFADLAMNYKHGDPIPKVEFTEEEIKTWGTVFQELNKLYPTHACREYLKNLPLLSKYCGYREDNIPQLEDVSNFLKERTGFSIRPVAGYLSPRDFLSGLAFRVFHCTQYVRHSSDPFYTPEPDTCHELLGHVPLLAEPSFAQFSQEIGLASLGASEEAVQKLATCYFFTVEFGLCKQDGQLRVFGAGLLSSISELKHALSGHAKVKPFDPKITCKQECLITTFQDVYFVSESFEDAKEKMREFTKTIKRPFGVKYNHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	4-[(N-{[2-(3-methoxyphenoxy)-6-(piperidin-1-yl)phenyl]methyl}carbamimidoyl)carbamoyl]-L-phenylalanine
Molecular weight formula_weight	545.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	140

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5j6da_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.178 — Aromatic aminoacid monoxygenases, catalytic and oligomerization domains
Superfamily Superfamily superfamily	d.178.1 — Aromatic aminoacid monoxygenases, catalytic and oligomerization domains
Family Family family	d.178.1.1 — Aromatic aminoacid monoxygenases, catalytic and oligomerization domains

Domain ID domain_id	d5j6db_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.178 — Aromatic aminoacid monoxygenases, catalytic and oligomerization domains
Superfamily Superfamily superfamily	d.178.1 — Aromatic aminoacid monoxygenases, catalytic and oligomerization domains
Family Family family	d.178.1.1 — Aromatic aminoacid monoxygenases, catalytic and oligomerization domains

CATH v4.4 (2 domains)

Domain ID domain_id	5j6dA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	800 — Phenylalanine Hydroxylase
Homologous superfamily homologous superfamily	10 — Aromatic amino acid hydroxylase

Domain ID domain_id	5j6dB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	800 — Phenylalanine Hydroxylase
Homologous superfamily homologous superfamily	10 — Aromatic amino acid hydroxylase

▶

Unit-cell length a length_a	58.726 Å
Unit-cell length b length_b	63.561 Å
Unit-cell length c length_c	156.468 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	8

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2117
R_work r_work	0.2098
R_free r_free	0.2481

Discovery of acyl guanidine tryptophan hydroxylase-1 inhibitors

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

Tryptophan 5-hydroxylase 1

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

5j6d__assembly_2__model_1

5j6d__assembly_2__model_1 | I(q)

5j6d__assembly_2__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Discovery of acyl guanidine tryptophan hydroxylase-1 inhibitors

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

Tryptophan 5-hydroxylase 1

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

5j6d__assembly_2__model_1

5j6d__assembly_2__model_1 | I(q)

5j6d__assembly_2__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)