SAXSdb — 4ldt

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

Ubiquitin thioesterase otubain-like

Caenorhabditis elegans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	Ubiquitin aldehyde × 1 （P0CG48） Ubiquitin-conjugating enzyme E2 D2 × 1 （P62837） Ubiquitin × 1 （P0CG48） 1,2-ETHANEDIOL × 4 MAGNESIUM ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OTUB1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–45； UniProt 1–45

Ubiquitin thioesterase otubain-like

Caenorhabditis elegans

UniProt Q9XVR6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	Ubiquitin aldehyde × 1 （P0CG48） Ubiquitin-conjugating enzyme E2 D2 × 1 （P62837） Ubiquitin × 1 （P0CG48） 1,2-ETHANEDIOL × 4 MAGNESIUM ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OTUBL_CAEEL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 46–288； UniProt 42–284

Ubiquitin aldehyde

Homo sapiens

UniProt P0CG48

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	Ubiquitin thioesterase otubain-like × 1 （Q96FW1,Q9XVR6） Ubiquitin-conjugating enzyme E2 D2 × 1 （P62837） 1,2-ETHANEDIOL × 4 MAGNESIUM ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBC_HUMAN
Isoform	—
PDB entities	2, 4
Chains and sequence ranges	Author chain B； PDBConstruct 1–76； UniProt 1–76 Author chain D； PDBConstruct 1–76； UniProt 1–76

Ubiquitin-conjugating enzyme E2 D2

Homo sapiens

UniProt P62837

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	Ubiquitin thioesterase otubain-like × 1 （Q96FW1,Q9XVR6） Ubiquitin aldehyde × 1 （P0CG48） Ubiquitin × 1 （P0CG48） 1,2-ETHANEDIOL × 4 MAGNESIUM ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UB2D2_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 2–148； 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	4ldt
Deposition date deposition_date	2013-06-25
Structure title title	The structure of h/ceOTUB1-ubiquitin aldehyde-UBCH5B~Ub
Keywords keywords	isopeptidase, ubiquitin-conjugating, post-translational modification, ubiquitin, ubiquitin-aldehyde, HYDROLASE REGULATOR; HYDROLASE REGULATOR
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.

4ldt__assembly_1__model_1

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

Download this curve (.dat)

4ldt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ldt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.42 Å
Rg (electron density)	25.37 Å
Total Rg	26.20 Å
Atom count	4379
Residues	554
Excluded volume	78296 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ldt__assembly_1__model_1`	tetrameric （4）	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 (7)

Entity 1 Entity 1 polymer

Description description	Ubiquitin thioesterase otubain-like
Molecular weight formula_weight	32795.6 kDa
EC 编号 ec_number	3.4.19.12
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	4832

MAAEEPQQQKQEPLGSDSEGVNCLAYDEAIMAQQDRIQQEIAVQNPLVATLAPFSILCAEYDNETSAAFLSKATELSEVYGEIRYIRGDGNCFYRAILVGLIEIMLKDRARLEKFIASSRDWTRTLVELGFPDWTCTDFCDFFIEFLEKIHSGVHTEEAVYTILNDDGSANYILMFFRLITSAFLKQNSEEYAPFIDEGMTVAQYCEQEIEPMWKDADHLAINSLIKAAGTRVRIEYMDRTAAPNGGWHYDIPSDDQQIAPEITLLYRPGHYDVIYKKDSTEASEIEN

Source Source

Source organism organism	Caenorhabditis elegans
Common name common_name	human, nematode
NCBI taxonomy ID ncbi_taxonomy_id	6239
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ubiquitin aldehyde
Molecular weight formula_weight	8560.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

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

Entity 3 Entity 3 polymer

Description description	Ubiquitin-conjugating enzyme E2 D2
Molecular weight formula_weight	16796.2 kDa
EC 编号 ec_number	6.3.2.19
Mutation mutation	C85S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GMALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSISLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM

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

Entity 4 Entity 4 polymer

Description description	Ubiquitin
Molecular weight formula_weight	8576.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

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

Entity 5 Entity 5 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 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	316

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4ldtb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d4ldtc1
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	d4ldtc2
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

Domain ID domain_id	d4ldtd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

CATH v4.4 (5 domains)

Domain ID domain_id	4ldtA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	60 — Peptidase C65 Otubain, subdomain 1

Domain ID domain_id	4ldtA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1300 — 3 helical TM bundles of succinate and fumarate reductases
Homologous superfamily homologous superfamily	20 — Peptidase C65 Otubain, subdomain 2

Domain ID domain_id	4ldtB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	4ldtC00
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	4ldtD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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Unit-cell length a length_a	104.894 Å
Unit-cell length b length_b	131.612 Å
Unit-cell length c length_c	46.501 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.901 Å
Low-resolution limit resolution_low	33.650 Å
R factor r_factor	0.1934
R_work r_work	0.1918
R_free r_free	0.2232

The structure of h/ceOTUB1-ubiquitin aldehyde-UBCH5B~Ub

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

Ubiquitin thioesterase otubain-like

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquitin thioesterase otubain-like

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquitin aldehyde

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquitin-conjugating enzyme E2 D2

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

4ldt__assembly_1__model_1

4ldt__assembly_1__model_1 | I(q)

4ldt__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (4 domains)

CATH v4.4 (5 domains)

7. Citations (1)