3d04

Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Helicobacter pylori in complex with sakuranetin

Method: X-RAY DIFFRACTION

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

(3R)-hydroxymyristoyl-acyl carrier protein dehydratase

Helicobacter pylori

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	CHLORIDE ION × 6 BENZAMIDINE × 6 (2S)-5-hydroxy-2-(4-hydroxyphenyl)-7-methoxy-2,3-dihydro-4H-chromen-4-one × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5G940_HELPY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–159； UniProt 1–159 Author chain B； PDBConstruct 1–159； UniProt 1–159 Author chain C； PDBConstruct 1–159； UniProt 1–159 Author chain D； PDBConstruct 1–159； UniProt 1–159 Author chain E； PDBConstruct 1–159； UniProt 1–159 Author chain F； PDBConstruct 1–159； UniProt 1–159

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	3d04
Deposition date deposition_date	2008-05-01
Structure title title	Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Helicobacter pylori in complex with sakuranetin
Keywords keywords	FabZ complex, sakuranetin, Lyase; LYASE
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.

3d04__assembly_1__model_1

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

Download this curve (.dat)

3d04__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3d04__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.80 Å
Rg (electron density)	27.60 Å
Total Rg	28.72 Å
Atom count	7374
Residues	903
Excluded volume	133680 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3d04__assembly_1__model_1`	hexameric （6）	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 (5)

Entity 1 Entity 1 polymer

Description description	(3R)-hydroxymyristoyl-acyl carrier protein dehydratase
Molecular weight formula_weight	18206.1 kDa
EC 编号 ec_number	4.2.1.-
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	7813

MEQSHQNLQSQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAERE

Source Source

Source organism organism	Helicobacter pylori
NCBI taxonomy ID ncbi_taxonomy_id	210
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	BENZAMIDINE
Molecular weight formula_weight	120.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	(2S)-5-hydroxy-2-(4-hydroxyphenyl)-7-methoxy-2,3-dihydro-4H-chromen-4-one
Molecular weight formula_weight	286.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	439

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3d04a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.6 — FabZ-like

Domain ID domain_id	d3d04b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.6 — FabZ-like

Domain ID domain_id	d3d04c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.6 — FabZ-like

Domain ID domain_id	d3d04d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.6 — FabZ-like

Domain ID domain_id	d3d04e_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.6 — FabZ-like

Domain ID domain_id	d3d04f_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.6 — FabZ-like

CATH v4.4 (6 domains)

Domain ID domain_id	3d04A00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

Domain ID domain_id	3d04B00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

Domain ID domain_id	3d04C00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

Domain ID domain_id	3d04D00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

Domain ID domain_id	3d04E00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

Domain ID domain_id	3d04F00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

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Unit-cell length a length_a	73.967 Å
Unit-cell length b length_b	100.312 Å
Unit-cell length c length_c	186.570 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	24

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	19.990 Å
R factor r_factor	0.1910
R_work r_work	0.1900
R_free r_free	0.2120

Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Helicobacter pylori in complex with sakuranetin

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

(3R)-hydroxymyristoyl-acyl carrier protein dehydratase

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

3d04__assembly_1__model_1

3d04__assembly_1__model_1 | I(q)

3d04__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Helicobacter pylori in complex with sakuranetin

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

(3R)-hydroxymyristoyl-acyl carrier protein dehydratase

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

3d04__assembly_1__model_1

3d04__assembly_1__model_1 | I(q)

3d04__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)