SAXSdb — 6qgn

▼

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

Acyl-protein thioesterase 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	2-Bromopalmitic acid × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	2-Bromopalmitic acid × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	2-Bromopalmitic acid × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	2-Bromopalmitic acid × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LYPA1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–233； UniProt 1–230 Author chain B； PDBConstruct 4–233； UniProt 1–230 Author chain C； PDBConstruct 4–233； UniProt 1–230 Author chain D； PDBConstruct 4–233； UniProt 1–230

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	6qgn
Deposition date deposition_date	2019-01-12
Structure title title	Crystal structure of APT1 bound to 2-Bromopalmitate
Keywords keywords	acyl-protein thioesterase 2-bromopalmitate Depalmitoylation, HYDROLASE; HYDROLASE
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.

6qgn__assembly_1__model_1

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

Download this curve (.dat)

6qgn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6qgn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.70 Å
Rg (electron density)	16.33 Å
Total Rg	17.53 Å
Atom count	1745
Residues	223
Excluded volume	30598 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6qgn__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6qgn__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6qgn__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6qgn__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Acyl-protein thioesterase 1
Molecular weight formula_weight	24977.8 kDa
EC 编号 ec_number	3.1.2.-
Mutation mutation	C2S
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7636

GSRMSGNNMSTPLPAIVPAARKATAAVIFLHGLGDTGHGWAEAFAGIRSSHIKYICPHAPVRPVTLNMNVAMPSWFDIIGLSPDSQEDESGIKQAAENIKALIDQEVKNGIPSNRIILGGFSQGGALSLYTALTTQQKLAGVTALSCWLPLRASFPQGPIGGANRDISILQCHGDCDPLVPLMFGSLTVEKLKTLVNPANVTFKTYEGMMHSSCQQEMMDVKQFIDKLLPPID

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	2-Bromopalmitic acid
Molecular weight formula_weight	335.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	438

▼

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6qgna_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.0 — automated matches

Domain ID domain_id	d6qgnb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.0 — automated matches

Domain ID domain_id	d6qgnc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.0 — automated matches

Domain ID domain_id	d6qgnd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	6qgnA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	6qgnB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	6qgnC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	6qgnD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

▶

Unit-cell length a length_a	58.900 Å
Unit-cell length b length_b	109.616 Å
Unit-cell length c length_c	174.713 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	16

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

Resolution resolution	2.099 Å
Low-resolution limit resolution_low	46.427 Å
R factor r_factor	0.2322
R_work r_work	0.2300
R_free r_free	0.2733

Crystal structure of APT1 bound to 2-Bromopalmitate

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

Acyl-protein thioesterase 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

6qgn__assembly_1__model_1

6qgn__assembly_1__model_1 | I(q)

6qgn__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 (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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of APT1 bound to 2-Bromopalmitate

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

Acyl-protein thioesterase 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

6qgn__assembly_1__model_1

6qgn__assembly_1__model_1 | I(q)

6qgn__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 (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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)