SAXSdb — 1z2u

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

Ubiquitin-conjugating enzyme E2 2

Caenorhabditis elegans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 6 SODIUM ION × 1 (R,R)-2,3-BUTANEDIOL × 2 UNKNOWN ATOM OR ION × 10 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBC2_CAEEL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–150； UniProt 1–147

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	1z2u
Deposition date deposition_date	2005-03-09
Structure title title	The 1.1A crystallographic structure of ubiquitin-conjugating enzyme (ubc-2) from Caenorhabditis elegans: functional and evolutionary significance
Keywords keywords	;PSI, SECSG, ubiquitin-conjugating enzyme, Caenorhabditis elegans, proteosome pathway, Structural Genomics, Protein Structure Initiative, Southeast Collaboratory for Structural Genomics, LIGASE ;; LIGASE
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.

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1z2u__assembly_1__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Ubiquitin-conjugating enzyme E2 2
Molecular weight formula_weight	17005.4 kDa
EC 编号 ec_number	6.3.2.19
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	1409

GSHMALKRIQKELQDLGRDPPAQCSAGPVGDDLFHWQATIMGPPESPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDRERYNQLAREWTQKYAM

Source Source

Source organism organism	Caenorhabditis elegans
NCBI taxonomy ID ncbi_taxonomy_id	6239
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	(R,R)-2,3-BUTANEDIOL
Molecular weight formula_weight	90.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	UNKNOWN ATOM OR ION
Source method src_method	syn
Copy count entity_count	10

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	113

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1z2ua1
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.20.1.1 — UBC-related

Domain ID domain_id	d1z2ua2
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 (1 domains)

Domain ID domain_id	1z2uA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

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Unit-cell length a length_a	29.604 Å
Unit-cell length b length_b	60.457 Å
Unit-cell length c length_c	43.980 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.45 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.100 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.1305
R_free r_free	0.1493

The 1.1A crystallographic structure of ubiquitin-conjugating enzyme (ubc-2) from Caenorhabditis elegans: functional and evolutionary significance

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

Ubiquitin-conjugating enzyme E2 2

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

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)

The 1.1A crystallographic structure of ubiquitin-conjugating enzyme (ubc-2) from Caenorhabditis elegans: functional and evolutionary significance

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

Ubiquitin-conjugating enzyme E2 2

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

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)