SAXSdb — 2y9m

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

UBIQUITIN-CONJUGATING ENZYME E2-21 KDA

SACCHAROMYCES CEREVISIAE

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	PEROXISOME ASSEMBLY PROTEIN 22 × 1 （P39718） 1,2-ETHANEDIOL × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBCX_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–172； UniProt 15–183

PEROXISOME ASSEMBLY PROTEIN 22

SACCHAROMYCES CEREVISIAE

UniProt P39718

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	UBIQUITIN-CONJUGATING ENZYME E2-21 KDA × 1 （P29340） 1,2-ETHANEDIOL × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PEX22_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–130； UniProt 54–180

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	2y9m
Deposition date deposition_date	2011-02-15
Structure title title	Pex4p-Pex22p structure
Keywords keywords	;LIGASE-TRANSPORT PROTEIN COMPLEX, UBIQUITIN CONJUGATING ENZYME, E2 COMPLEX, PEROXISOMAL PROTEIN, ALPHA-BETA-ALPHA SANDWICH FOLD, E2 CO-ACTIVATOR ;; LIGASE/TRANSPORT PROTEIN
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.

2y9m__assembly_1__model_1

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

Download this curve (.dat)

2y9m__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2y9m__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.11 Å
Rg (electron density)	22.70 Å
Total Rg	23.80 Å
Atom count	2242
Residues	282
Excluded volume	40485 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2y9m__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	UBIQUITIN-CONJUGATING ENZYME E2-21 KDA
Molecular weight formula_weight	19573.5 kDa
EC 编号 ec_number	6.3.2.19
Mutation mutation	YES
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	2272

GAMADTCMSRIVKEYKVILKTLASDDPIANPYRGIIESLNPIDETDLSKWEAIISGPSDTPYENHQFRILIEVPSSYPMNPPKISFMQNNILHCNVKSATGEICLNILKPEEWTPVWDLLHCVHAVWRLLREPVCDSPLDVDIGNIIRCGDMSAYQGIVKYFLAERERINNH

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	PEROXISOME ASSEMBLY PROTEIN 22
Molecular weight formula_weight	14439.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GAMENKKARKSKCIIMSKSIQGLPIKWEEYAADEVVLLVPTSHTDGSMKQAIGDAFRKTKNEHKIIYCDSMDGLWSCVRRLGKFQCILNSRDFTSSGGSDAAVVPEDIGRFVKFVVDSDVEDVLIDTLCN

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 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	9

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2y9ma1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.0 — automated matches

Domain ID domain_id	d2y9ma2
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 (2 domains)

Domain ID domain_id	2y9mA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

Domain ID domain_id	2y9mB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11730 — Peroxisome assembly protein 22

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Unit-cell length a length_a	139.328 Å
Unit-cell length b length_b	43.194 Å
Unit-cell length c length_c	60.474 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.62 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2075
R_work r_work	0.2048
R_free r_free	0.2592

Pex4p-Pex22p structure

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

UBIQUITIN-CONJUGATING ENZYME E2-21 KDA

State in the Current Structure

Other States of the Same Protein in the Database

PEROXISOME ASSEMBLY PROTEIN 22

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

2y9m__assembly_1__model_1

2y9m__assembly_1__model_1 | I(q)

2y9m__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Pex4p-Pex22p structure

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

UBIQUITIN-CONJUGATING ENZYME E2-21 KDA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PEROXISOME ASSEMBLY PROTEIN 22

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

2y9m__assembly_1__model_1

2y9m__assembly_1__model_1 | I(q)

2y9m__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)