SAXSdb — 2v1r

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

PEROXISOMAL MEMBRANE PROTEIN PAS20

SACCHAROMYCES CEREVISIAE

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	PEX14 × 2 （P53112） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	PEX14 × 1 （P53112） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PEX13_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–80； UniProt 299–374 Author chain B； PDBConstruct 5–80； UniProt 299–374

PEX14

OrganismNot specified

UniProt P53112

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	PEROXISOMAL MEMBRANE PROTEIN PAS20 × 1 （P80667） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	PEROXISOMAL MEMBRANE PROTEIN PAS20 × 1 （P80667） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PEX14_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain P； PDBConstruct 2–15； UniProt 83–96 Author chain Q； PDBConstruct 2–15； UniProt 83–96 Author chain R； PDBConstruct 2–15； UniProt 83–96

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	2v1r
Deposition date deposition_date	2007-05-29
Structure title title	Yeast Pex13 SH3 domain complexed with a peptide from Pex14 at 2.1 A resolution
Keywords keywords	PROTEIN TRANSPORT, TRANSLOCATION, TRANSMEMBRANE, PEPTIDE COMPLEX, STRUCTURAL GENOMICS, PEROXISOME; PROTEIN TRANSPORT
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.

2v1r__assembly_2__model_1

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

Download this curve (.dat)

2v1r__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2v1r__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	13.89 Å
Rg (electron density)	12.46 Å
Total Rg	14.00 Å
Atom count	618
Residues	76
Excluded volume	11178 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2v1r__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2v1r__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	PEROXISOMAL MEMBRANE PROTEIN PAS20
Molecular weight formula_weight	9316.7 kDa
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	1369

ISEFGSEPIDPSKLEFARALYDFVPENPEMEVALKKGDLMAILSKKDPLGRDSDWWKVRTKNGNIGYIPYNYIEIIKRRK

Source Source

Source organism organism	SACCHAROMYCES CEREVISIAE
Common name common_name	;BAKER'S YEAST ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	PEX14
Molecular weight formula_weight	1722.0 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Q,R

XEAMPPTLPHRDWKD

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	105

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2v1ra_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.2 — SH3-domain
Family Family family	b.34.2.1 — SH3-domain

Domain ID domain_id	d2v1rb_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.2 — SH3-domain
Family Family family	b.34.2.1 — SH3-domain

CATH v4.4 (2 domains)

Domain ID domain_id	2v1rA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

Domain ID domain_id	2v1rB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

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Unit-cell length a length_a	36.440 Å
Unit-cell length b length_b	39.090 Å
Unit-cell length c length_c	39.140 Å
Unit-cell angle α angle_alpha	86.85 °
Unit-cell angle β angle_beta	65.46 °
Unit-cell angle γ angle_gamma	62.04 °
Molecules per unit cell Z z_pdb	3

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1912
R_free r_free	0.2286

Yeast Pex13 SH3 domain complexed with a peptide from Pex14 at 2.1 A resolution

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

PEROXISOMAL MEMBRANE PROTEIN PAS20

State in the Current Structure

Other States of the Same Protein in the Database

PEX14

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

2v1r__assembly_2__model_1

2v1r__assembly_2__model_1 | I(q)

2v1r__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 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Yeast Pex13 SH3 domain complexed with a peptide from Pex14 at 2.1 A resolution

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

PEROXISOMAL MEMBRANE PROTEIN PAS20

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PEX14

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

2v1r__assembly_2__model_1

2v1r__assembly_2__model_1 | I(q)

2v1r__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 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)