SAXSdb — 3w15

▼

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

Peroxisomal targeting signal 2 receptor

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3	Peroxisomal membrane protein PEX21 × 1 （P50091） 3-ketoacyl-CoA thiolase, peroxisomal, Maltose-binding periplasmic protein × 1 （P0AEX9,P27796） NITRATE ION × 9 MAGNESIUM ION × 6 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PEX7_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–368； UniProt 1–375

Peroxisomal membrane protein PEX21

Saccharomyces cerevisiae

UniProt P50091

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3	Peroxisomal targeting signal 2 receptor × 1 （P39108） 3-ketoacyl-CoA thiolase, peroxisomal, Maltose-binding periplasmic protein × 1 （P0AEX9,P27796） NITRATE ION × 9 MAGNESIUM ION × 6 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PEX21_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–101； UniProt 190–288

3-ketoacyl-CoA thiolase, peroxisomal, Maltose-binding periplasmic protein

Escherichia coli

UniProt P0AEX9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3	Peroxisomal targeting signal 2 receptor × 1 （P39108） Peroxisomal membrane protein PEX21 × 1 （P50091） NITRATE ION × 9 MAGNESIUM ION × 6 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MALE_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 20–389； UniProt 27–396

3-ketoacyl-CoA thiolase, peroxisomal, Maltose-binding periplasmic protein

Escherichia coli

UniProt P27796

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3	Peroxisomal targeting signal 2 receptor × 1 （P39108） Peroxisomal membrane protein PEX21 × 1 （P50091） NITRATE ION × 9 MAGNESIUM ION × 6 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THIK_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 3–17； UniProt 1–15

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	3w15
Deposition date deposition_date	2012-11-06
Structure title title	Structure of peroxisomal targeting signal 2 (PTS2) of Saccharomyces cerevisiae 3-ketoacyl-CoA thiolase in complex with Pex7p and Pex21p
Keywords keywords	beta-propeller, targeting signal recognition, cytosol, peroxisome, Protein Transport; PROTEIN TRANSPORT
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.

3w15__assembly_1__model_1

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

Download this curve (.dat)

3w15__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3w15__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.60 Å
Rg (electron density)	31.21 Å
Total Rg	31.80 Å
Atom count	6209
Residues	797
Excluded volume	109830 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3w15__assembly_1__model_1`	trimeric （3）	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	Peroxisomal targeting signal 2 receptor
Molecular weight formula_weight	41525.8 kDa
Mutation mutation	del(E257-V265)
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	6824

GSMLRYHMQGFSGYGVQYSPFFDNRLAVAAGSNFGLVGNGKLFILEIDRSGRIVEVNSFLTQDCLFDLAWNESHENQVLVAQGDGTLRLFDTTFKEFPIAIFKEHEREVFSCNWNLVNRQNFLSSSWDGSIKIWSPLRKQSLMTLTPRPLEITKMVDPLNAIILKKKSFTGISKNRNCVYQAQFSPHDQNLVLSCSGNSYASLFDIRLPSGKNQNNFLVHSGLEALTCDFNKYRPYVVATGGVDNAIRIWDIRMLNKNPGQLHNSSCINEIPNAHGLAIRKVTWSPHHSNILMSASYDMTCRIWRDLSNDGAKETYKTNSTDATKGSIFNFTQHSEFVFGADWSLWGKPGYVASTAWDGNLFVWNGLG

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Komagataella pastoris

Entity 2 Entity 2 polymer

Description description	Peroxisomal membrane protein PEX21
Molecular weight formula_weight	11004.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSKWFDQDQSELQRIATDIVKCCTPPPSSASSSSTLSSSVESKLSESKFIQLMRNISSGDVTLKKNADGNSASELFSSNNGELVGNRHIFVKDEIHKDILD

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	3-ketoacyl-CoA thiolase, peroxisomal, Maltose-binding periplasmic protein
Molecular weight formula_weight	42897.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GSMSQRLQSIKDHLVESRSKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRITK

Source Source

Source organism organism	Escherichia coli
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	NITRATE ION
Molecular weight formula_weight	62.0 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	563

▼

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3w15c1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

Domain ID domain_id	d3w15c2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id	3w15A01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	3w15B00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	3w15C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

▶

Unit-cell length a length_a	78.890 Å
Unit-cell length b length_b	52.750 Å
Unit-cell length c length_c	97.570 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.59 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	32.200 Å
R factor r_factor	0.1908
R_work r_work	0.1891
R_free r_free	0.2239

Structure of peroxisomal targeting signal 2 (PTS2) of Saccharomyces cerevisiae 3-ketoacyl-CoA thiolase in complex with Pex7p and Pex21p

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

Peroxisomal targeting signal 2 receptor

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Peroxisomal membrane protein PEX21

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

3-ketoacyl-CoA thiolase, peroxisomal, Maltose-binding periplasmic protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

3-ketoacyl-CoA thiolase, peroxisomal, Maltose-binding periplasmic protein

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

3w15__assembly_1__model_1

3w15__assembly_1__model_1 | I(q)

3w15__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)