SAXSdb — 2cm0

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

PEPTIDE N-GLYCANASE HOMOLOG

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	DI(HYDROXYETHYL)ETHER × 1 BETA-MERCAPTOETHANOL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9BVR8_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–99； UniProt 8–106

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	2cm0
Deposition date deposition_date	2006-05-03
Structure title title	The PUB domain functions as a p97 binding module in human peptide N-glycanase.
Keywords keywords	TRANSFERASE, KINASE, PUG DOMAIN; TRANSFERASE
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.

2cm0__assembly_1__model_1

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

Download this curve (.dat)

2cm0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2cm0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	14.28 Å
Rg (electron density)	12.79 Å
Total Rg	14.18 Å
Atom count	777
Residues	99
Excluded volume	13918 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2cm0__assembly_1__model_1`	monomeric （1）	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	PEPTIDE N-GLYCANASE HOMOLOG
Molecular weight formula_weight	10915.5 kDa
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	876

GSASPAVAELCQNTPETFLEASKLLLTYADAILRNPNDEAARSIRIGNTAFSTRLLPVRGAVECLFEMGFEEGETHLIFPKKASVEQLQKIRDLIAIER

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	ESCHERICHIA COLI BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	99

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2cm0a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.314 — PUG domain-like
Superfamily Superfamily superfamily	d.314.1 — PUG domain-like
Family Family family	d.314.1.1 — PUG domain

CATH v4.4 (1 domains)

Domain ID domain_id	2cm0A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

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Unit-cell length a length_a	73.987 Å
Unit-cell length b length_b	73.987 Å
Unit-cell length c length_c	32.994 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 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.1851
R_work r_work	0.1851
R_free r_free	0.2231

The PUB domain functions as a p97 binding module in human peptide N-glycanase.

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

PEPTIDE N-GLYCANASE HOMOLOG

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

2cm0__assembly_1__model_1

2cm0__assembly_1__model_1 | I(q)

2cm0__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

The PUB domain functions as a p97 binding module in human peptide N-glycanase.

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

PEPTIDE N-GLYCANASE HOMOLOG

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

2cm0__assembly_1__model_1

2cm0__assembly_1__model_1 | I(q)

2cm0__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)