SAXSdb — 5ejj

▼

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 monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	water × 2	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 1–564； UniProt 26–589 Author chain B； PDBConstruct 1–564； UniProt 26–589

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5ejj
Deposition date deposition_date	2015-11-02
Structure title title	Crystal structure of UfSP from C.elegans
Keywords keywords	Ufm1, UfSP, Deufmylation, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

5ejj__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5ejj__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ejj__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	26.06 Å
Rg (electron density)	24.96 Å
Total Rg	25.86 Å
Atom count	4169
Residues	520
Excluded volume	73916 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ejj__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5ejj__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5ejj__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Ufm1-specific protease
Molecular weight formula_weight	64095.2 kDa
EC 编号 ec_number	3.4.22.-
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	8530

NELWFIDAQAMFQNYANLRSFSKSNANEINTTIGGFVFGRKARKQVIHVLFAYAEDLTESNRQFLESSLSADIELVGNLNIDGQSQILPGGQFTLQLTSRMLENRSISEFLDMNVMFNNEHVLMEGASCVSRVGYEWSLRAGREQEDVKSAAERLSMASFRFTYLNAEHGLVIREQKPEAAQQKYLDKFSKGAVPYKDVIEFTAMQSLTRDTSNDTEDQKLVPTVKVTKDNKHFTRLVTIGEVVFPAFFGDSSLDLYKRSREAFNRRANNTMMVTVNGIRAGRGVTTTTSATYLPPGWVSLLHLQLPTKWTDNEQRNYRIRLHKLFNLPSSKPVLRLSQALALHSESARLTNKKLIREPHLSITNYQPVGEITTVNGPYNYHHYMQDGIDDSGWGCAYRSFQTIWSWFILNGYTDKPVPSHREIQQALVDIQDKQAKFVGSRQWIGSTEISFVLNELLKLECRFIATNSGAEVVERVRELARHFETSGTPVMIGGNMLAHTILGVDFNDTTGETKFLVLDPHYTGSEDIKTITSKGWCAWKPASFWSKDHFYNMVLPQPPSDAI

Source Source

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

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	223

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5ejjA01
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	5ejjB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	130 —

▶

Unit-cell length a length_a	77.531 Å
Unit-cell length b length_b	149.808 Å
Unit-cell length c length_c	226.420 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	2.800 Å
Low-resolution limit resolution_low	41.278 Å
R factor r_factor	0.2066
R_work r_work	0.2056
R_free r_free	0.2369

Crystal structure of UfSP from C.elegans

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5ejj__assembly_2__model_1

5ejj__assembly_2__model_1 | I(q)

5ejj__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of UfSP from C.elegans

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5ejj__assembly_2__model_1

5ejj__assembly_2__model_1 | I(q)

5ejj__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)