SAXSdb — 5xda

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

Ufm1-specific protease

Caenorhabditis elegans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	Ubiquitin-fold modifier 1 × 6 （P34661） water × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UFSP_CAEEL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–565； UniProt 25–589 Author chain B； PDBConstruct 1–565； UniProt 25–589 Author chain C； PDBConstruct 1–565； UniProt 25–589 Author chain D； PDBConstruct 1–565； UniProt 25–589 Author chain E； PDBConstruct 1–565； UniProt 25–589 Author chain F； PDBConstruct 1–565； UniProt 25–589

Ubiquitin-fold modifier 1

Caenorhabditis elegans

UniProt P34661

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	Ufm1-specific protease × 6 （Q94218） water × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UFM1_CAEEL
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 1–84； UniProt 11–94 Author chain H； PDBConstruct 1–84； UniProt 11–94 Author chain I； PDBConstruct 1–84； UniProt 11–94 Author chain J； PDBConstruct 1–84； UniProt 11–94 Author chain K； PDBConstruct 1–84； UniProt 11–94 Author chain L； PDBConstruct 1–84； UniProt 11–94

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	5xda
Deposition date deposition_date	2017-03-28
Structure title title	Structural basis for Ufm1 recognition by UfSP
Keywords keywords	complex, molecular recognition, HYDROLASE; 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.

5xda__assembly_1__model_1

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

Download this curve (.dat)

5xda__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5xda__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	92.48 Å
Rg (electron density)	93.65 Å
Total Rg	93.60 Å
Atom count	29632
Residues	3732
Excluded volume	526290 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5xda__assembly_1__model_1`	dodecameric （12）	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	Ufm1-specific protease
Molecular weight formula_weight	64178.3 kDa
EC 编号 ec_number	3.4.22.-
Mutation mutation	C407S
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	29730

VNELWFIDAQAMFQNYANLRSFSKSNANEINTTIGGFVFGRKARKQVIHVLFAYAEDLTESNRQFLESSLSADIELVGNLNIDGQSQILPGGQFTLQLTSRMLENRSISEFLDMNVMFNNEHVLMEGASCVSRVGYEWSLRAGREQEDVKSAAERLSMASFRFTYLNAEHGLVIREQKPEAAQQKYLDKFSKGAVPYKDVIEFTAMQSLTRDTSNDTEDQKLVPTVKVTKDNKHFTRLVTIGEVVFPAFFGDSSLDLYKRSREAFNRRANNTMMVTVNGIRAGRGVTTTTSATYLPPGWVSLLHLQLPTKWTDNEQRNYRIRLHKLFNLPSSKPVLRLSQALALHSESARLTNKKLIREPHLSITNYQPVGEITTVNGPYNYHHYMQDGIDDSGWGSAYRSFQTIWSWFILNGYTDKPVPSHREIQQALVDIQDKQAKFVGSRQWIGSTEISFVLNELLKLECRFIATNSGAEVVERVRELARHFETSGTPVMIGGNMLAHTILGVDFNDTTGETKFLVLDPHYTGSEDIKTITSKGWCAWKPASFWSKDHFYNMVLPQPPSDAI

Source Source

Source organism organism	Caenorhabditis elegans
NCBI taxonomy ID ncbi_taxonomy_id	6239
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ubiquitin-fold modifier 1
Molecular weight formula_weight	8873.2 kDa
Mutation mutation	H94G
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I,J,K,L

GSKVTFKITLTSDPKLPFKVLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGVGVNPAQPAGNIFLKHGSELRLIPRDRVGG

Source Source

Source organism organism	Caenorhabditis elegans
NCBI taxonomy ID ncbi_taxonomy_id	6239
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	98

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	5xdaA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	5xdaB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	5xdaC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	5xdaD01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	5xdaE01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	5xdaF01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	5xdaG00
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	5xdaH00
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	5xdaI00
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	5xdaJ00
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	5xdaK00
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	5xdaL00
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	267.447 Å
Unit-cell length b length_b	455.326 Å
Unit-cell length c length_c	195.558 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	48

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.285 Å
Low-resolution limit resolution_low	46.165 Å
R factor r_factor	0.2070
R_work r_work	0.2066
R_free r_free	0.2432

Structural basis for Ufm1 recognition by UfSP

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

Ufm1-specific protease

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-fold modifier 1

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

5xda__assembly_1__model_1

5xda__assembly_1__model_1 | I(q)

5xda__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) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Structural basis for Ufm1 recognition by UfSP

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

Ufm1-specific protease

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-fold modifier 1

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

5xda__assembly_1__model_1

5xda__assembly_1__model_1 | I(q)

5xda__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) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)