SAXSdb — 2y9p

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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） water × 1	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） water × 1	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	2y9p
Deposition date deposition_date	2011-02-16
Structure title title	Pex4p-Pex22p mutant II structure
Keywords keywords	LIGASE-TRANSPORT PROTEIN COMPLEX, E2 COMPLEX, 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.

2y9p__assembly_1__model_1

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

Download this curve (.dat)

2y9p__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2y9p__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.39 Å
Rg (electron density)	22.89 Å
Total Rg	23.88 Å
Atom count	2201
Residues	289
Excluded volume	39572 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2y9p__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 (3)

Entity 1 Entity 1 polymer

Description description	UBIQUITIN-CONJUGATING ENZYME E2-21 KDA
Molecular weight formula_weight	19530.4 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	2204

GAMADTCMSRIVKEYKVILKTLASDDPIANPYRGIIESLNPIDETDLSKWEAIISGPSDTPYENHQFRILIEVPSSYPMNPPKISFMQNNILHCNVKSATGEICLNILKPEEWTPVWDLLHCVHAVWRLLREPVCDSPLDVDIGAIIRCGDMSAYQGIVKYFLAERERINNH

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2y9pA00
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	2y9pB00
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	114.002 Å
Unit-cell length b length_b	41.630 Å
Unit-cell length c length_c	71.117 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.46 °
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	3.250 Å
Low-resolution limit resolution_low	47.540 Å
R factor r_factor	0.2099
R_work r_work	0.2072
R_free r_free	0.2676

Pex4p-Pex22p mutant II 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

2y9p__assembly_1__model_1

2y9p__assembly_1__model_1 | I(q)

2y9p__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Pex4p-Pex22p mutant II 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

2y9p__assembly_1__model_1

2y9p__assembly_1__model_1 | I(q)

2y9p__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)