SAXSdb — 3esw

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

Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 2 其他Polymer 1	UV excision repair protein RAD23 × 1 （P32628） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ZINC ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PNG1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–355； UniProt 8–341

UV excision repair protein RAD23

Saccharomyces cerevisiae

UniProt P32628

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 2 其他Polymer 1	Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase × 1 （Q02890） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ZINC ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAD23_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–55； UniProt 254–308

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	3esw
Deposition date deposition_date	2008-10-06
Structure title title	Complex of yeast PNGase with GlcNAc2-IAc.
Keywords keywords	;Glycoproteins Peptide:N-glycanase Chitobiose, Hydrolase, Metal-binding, Nucleus, DNA damage, DNA repair, Phosphoprotein, Ubl conjugation pathway ;; HYDROLASE
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.

3esw__assembly_1__model_1

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

Download this curve (.dat)

3esw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3esw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.53 Å
Rg (electron density)	25.99 Å
Total Rg	26.84 Å
Atom count	3213
Residues	387
Excluded volume	57054 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3esw__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 (5)

Entity 1 Entity 1 polymer

Description description	Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase
Molecular weight formula_weight	41698.1 kDa
EC 编号 ec_number	3.5.1.52
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	3220

MGSSHHHHHHSSGLVPRGSHMNNIDFDSIAKMLLIKYKDFILSKFKKAAPVENIRFQNLVHTNQFAQGVLGQSQHLCTVYDNPSWHSIVLETLDLDLIYKNVDKEFAKDGHAEGENIYTDYLVKELLRYFKQDFFKWCNKPDCNHCGQNTSENMTPLGSQGPNGEESKFNCGTVEIYKCNRCGNITRFPRYNDPIKLLETRKGRCGEWCNLFTLILKSFGLDVRYVWNREDHVWCEYFSNFLNRWVHVDSCEQSFDQPYIYSINWNKKMSYCIAFGKDGVVDVSKRYILQNELPRDQIKEEDLKFLCQFITKRLRYSLNDDEIYQLACRDEQEQIELIRGKTQETKSESVSAASK

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	UV excision repair protein RAD23
Molecular weight formula_weight	6050.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SIGLTVEDLLSLRQVVSGNPEALAPLLENISARYPQLREHIMANPEVFVSMLLEA

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	7

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	3eswA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	620 — C8orf32 fold
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	3eswA02
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3eswB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	540 — XPC-binding domain

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Unit-cell length a length_a	131.530 Å
Unit-cell length b length_b	131.530 Å
Unit-cell length c length_c	127.751 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	3.400 Å
Low-resolution limit resolution_low	37.960 Å
R factor r_factor	0.1990
R_work r_work	0.1970
R_free r_free	0.2350

Complex of yeast PNGase with GlcNAc2-IAc.

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

Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase

State in the Current Structure

Other States of the Same Protein in the Database

UV excision repair protein RAD23

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

3esw__assembly_1__model_1

3esw__assembly_1__model_1 | I(q)

3esw__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Complex of yeast PNGase with GlcNAc2-IAc.

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

Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

UV excision repair protein RAD23

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

3esw__assembly_1__model_1

3esw__assembly_1__model_1 | I(q)

3esw__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)