SAXSdb — 4pkb

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

Patatin-17

Solanum cardiophyllum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	METHYL ARACHIDONYL FLUOROPHOSPHONATE × 1 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	METHYL ARACHIDONYL FLUOROPHOSPHONATE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PAT17_SOLCD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 10–373； UniProt 23–386

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	4pkb
Deposition date deposition_date	2014-05-14
Structure title title	CRYSTAL STRUCTURE OF PATATIN-17 COMPLEXED WITH METHYL ARACHIDONYL FLUOROPHOSPHONATE (MAFP)
Keywords keywords	ALPHA/BETA CLASS FOLD WITH APPROXIMATELY THREE LAYERS, SERINE HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
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.

4pkb__assembly_2__model_1

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

Download this curve (.dat)

4pkb__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4pkb__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	26.29 Å
Rg (electron density)	24.96 Å
Total Rg	25.87 Å
Atom count	5542
Residues	714
Excluded volume	98903 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4pkb__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4pkb__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	Patatin-17
Molecular weight formula_weight	41264.5 kDa
EC 编号 ec_number	3.1.1.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2929

MHHHHHHAMAQLGEMVTVLSIDGGGIRGIIPATILEFLEGQLQEMDNNADARLADYFDVIGGTSTGGLLTAMISTPNENNRPFAAAKEIVPFYFEHGPQIFNPSGQILGPKYDGKYLMQVLQEKLGETRVHQALTEVVISSFDIKTNKPVIFTKSNLANSPELDAKMYDISYSTAAAPTYFPPHYFVTNTSNGDEYEFNLVDGAVATVADPALLSISVATRLAQKDPAFASIRSLNYKKMLLLSLGTGTTSEFDKTYTAKEAATWTAVHWMLVIQKMTDAASSYMTDYYLSTAFQALDSKNNYLRVQENALTGTTTEMDDASEANMELLVQVGENLLKKPVSEDNPETYEEALKRFAKLLSDRKKLRANKASY

Source Source

Source organism organism	Solanum cardiophyllum
Common name common_name	Heartleaf nightshade
NCBI taxonomy ID ncbi_taxonomy_id	160510
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	METHYL ARACHIDONYL FLUOROPHOSPHONATE
Molecular weight formula_weight	370.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	158

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4pkba_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.19 — FabD/lysophospholipase-like
Superfamily Superfamily superfamily	c.19.1 — FabD/lysophospholipase-like
Family Family family	c.19.1.3 — Patatin

CATH v4.4 (1 domains)

Domain ID domain_id	4pkbA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1090 — Cytosolic phospholipase A2 catalytic domain
Homologous superfamily homologous superfamily	10 — Cytosolic phospholipase A2 catalytic domain

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Unit-cell length a length_a	53.240 Å
Unit-cell length b length_b	53.240 Å
Unit-cell length c length_c	245.010 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.090 Å
Low-resolution limit resolution_low	22.257 Å
R factor r_factor	0.1780
R_work r_work	0.1760
R_free r_free	0.2120

CRYSTAL STRUCTURE OF PATATIN-17 COMPLEXED WITH METHYL ARACHIDONYL FLUOROPHOSPHONATE (MAFP)

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

Patatin-17

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

4pkb__assembly_2__model_1

4pkb__assembly_2__model_1 | I(q)

4pkb__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF PATATIN-17 COMPLEXED WITH METHYL ARACHIDONYL FLUOROPHOSPHONATE (MAFP)

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

Patatin-17

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

4pkb__assembly_2__model_1

4pkb__assembly_2__model_1 | I(q)

4pkb__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)