SAXSdb — 4kdi

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

Transitional endoplasmic reticulum ATPase

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin thioesterase OTU1 × 1 （P43558） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin thioesterase OTU1 × 1 （P43558） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TERA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 18–193； UniProt 21–196 Author chain B； PDBConstruct 18–193； UniProt 21–196

Ubiquitin thioesterase OTU1

Saccharomyces cerevisiae

UniProt P43558

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Transitional endoplasmic reticulum ATPase × 1 （P55072） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Transitional endoplasmic reticulum ATPase × 1 （P55072） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OTU1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 18–90； UniProt 1–73 Author chain D； PDBConstruct 18–90； UniProt 1–73

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	4kdi
Deposition date deposition_date	2013-04-25
Structure title title	Crystal structure of p97/VCP N in complex with OTU1 UBXL
Keywords keywords	AAA ATPase, PROTEIN-PROTEIN COMPLEX, UBX-like domain, PROTEIN BINDING, beta-barrel, beta-grasp, SIGNALING PROTEIN-HYDROLASE complex; SIGNALING PROTEIN/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.

4kdi__assembly_1__model_1

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

Download this curve (.dat)

4kdi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4kdi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.39 Å
Rg (electron density)	18.23 Å
Total Rg	19.24 Å
Atom count	1772
Residues	222
Excluded volume	31790 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4kdi__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4kdi__assembly_2__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	Transitional endoplasmic reticulum ATPase
Molecular weight formula_weight	21806.0 kDa
EC 编号 ec_number	3.6.4.6
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3863

GSHMASMTGGQQMGRGSNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEE

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 2 Entity 2 polymer

Description description	Ubiquitin thioesterase OTU1
Molecular weight formula_weight	9694.0 kDa
EC 编号 ec_number	3.4.19.12
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

GSHMASMTGGQQMGRGSMKLKVTGAGINQVVTLKQDATLNDLIEHINVDVKTMRFGYPPQRINLQGEDASLGQTQLDELGINSGEKITIE

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
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	198

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4kdia1
Class class	b — All beta proteins
Fold Fold fold	b.52 — Double psi beta-barrel
Superfamily Superfamily superfamily	b.52.2 — ADC-like
Family Family family	b.52.2.3 — Cdc48 N-terminal domain-like

Domain ID domain_id	d4kdia2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.31 — Cdc48 domain 2-like
Superfamily Superfamily superfamily	d.31.1 — Cdc48 domain 2-like
Family Family family	d.31.1.1 — Cdc48 domain 2-like

Domain ID domain_id	d4kdib1
Class class	b — All beta proteins
Fold Fold fold	b.52 — Double psi beta-barrel
Superfamily Superfamily superfamily	b.52.2 — ADC-like
Family Family family	b.52.2.3 — Cdc48 N-terminal domain-like

Domain ID domain_id	d4kdib2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.31 — Cdc48 domain 2-like
Superfamily Superfamily superfamily	d.31.1 — Cdc48 domain 2-like
Family Family family	d.31.1.1 — Cdc48 domain 2-like

CATH v4.4 (6 domains)

Domain ID domain_id	4kdiA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4kdiA02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	330 — Vcp-like ATPase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4kdiB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4kdiB02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	330 — Vcp-like ATPase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4kdiC00
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	4kdiD00
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	42.819 Å
Unit-cell length b length_b	88.609 Å
Unit-cell length c length_c	143.535 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.860 Å
Low-resolution limit resolution_low	42.340 Å
R factor r_factor	0.2158
R_work r_work	0.2137
R_free r_free	0.2568

Crystal structure of p97/VCP N in complex with OTU1 UBXL

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

Transitional endoplasmic reticulum ATPase

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin thioesterase OTU1

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

4kdi__assembly_1__model_1

4kdi__assembly_1__model_1 | I(q)

4kdi__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) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of p97/VCP N in complex with OTU1 UBXL

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

Transitional endoplasmic reticulum ATPase

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 OTU1

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

4kdi__assembly_1__model_1

4kdi__assembly_1__model_1 | I(q)

4kdi__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) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)