SAXSdb — 1p0r

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

ubiquitin-like 5

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–73	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 5.7；298 K；Ionic strength (raw mmCIF value) 50mM sodium phosphate；Pressure ambient NMR sample composition：.5mM UBL5 U-15N,13C 50mM sodium phosphate (pH 5.7), 2mM Dtt \| 90% H2O/10% D2O NMR sample composition：1.0mM UBL5 U-15N,13C 50mM sodium phosphate (pH 5.7), 2mM Dtt \| 100% D2O	Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1P0R	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4PYU The conserved ubiquitin-like protein hub1 plays a critical role in splicing in human cells Deposited 2014-03-28	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–73（73 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；0.1 M TRIS-HCL, 0.15 M SODIUM ACETATE, 20% W/V PEG4000, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.246
4PYU The conserved ubiquitin-like protein hub1 plays a critical role in splicing in human cells Deposited 2014-03-28	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–73（73 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；0.1 M TRIS-HCL, 0.15 M SODIUM ACETATE, 20% W/V PEG4000, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.246
4PYU The conserved ubiquitin-like protein hub1 plays a critical role in splicing in human cells Deposited 2014-03-28	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1–73（73 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；0.1 M TRIS-HCL, 0.15 M SODIUM ACETATE, 20% W/V PEG4000, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.246
4PYU The conserved ubiquitin-like protein hub1 plays a critical role in splicing in human cells Deposited 2014-03-28	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 1–73（73 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；0.1 M TRIS-HCL, 0.15 M SODIUM ACETATE, 20% W/V PEG4000, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.246
4PYU The conserved ubiquitin-like protein hub1 plays a critical role in splicing in human cells Deposited 2014-03-28	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain O 1–73（73 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；0.1 M TRIS-HCL, 0.15 M SODIUM ACETATE, 20% W/V PEG4000, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.246
4PYU The conserved ubiquitin-like protein hub1 plays a critical role in splicing in human cells Deposited 2014-03-28	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain S 1–73（73 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；0.1 M TRIS-HCL, 0.15 M SODIUM ACETATE, 20% W/V PEG4000, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.246
6AHD The Cryo-EM Structure of Human Pre-catalytic Spliceosome (B complex) at 3.8 angstrom resolution Deposited 2018-08-17	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 63-meric	Chain A0 1–73（73 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7AAV Human pre-Bact-2 spliceosome core structure Deposited 2020-09-04	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 13 PDB declaration: heptadecameric	Chain q 1–73（73 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 KGN D-chiro inositol hexakisphosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
7ABF Human pre-Bact-1 spliceosome core structure Deposited 2020-09-07	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: pentadecameric	Chain q 1–73（73 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
7ABG Human pre-Bact-1 spliceosome Deposited 2020-09-07	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric	Chain q 1–73（73 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GTG 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.80 Å
7ABI Human pre-Bact-2 spliceosome Deposited 2020-09-07	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric	Chain q 1–73（73 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.00 Å
8H6K Cryo-EM structure of human exon-defined spliceosome in the mature B state. Deposited 2022-10-18	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 63-meric	Chain 4M 1–73（73 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8Q7N cryo-EM structure of the human spliceosomal B complex protomer (tri-snRNP core region) Deposited 2023-08-16	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 17 PDB declaration: 21-meric	Chain s 1–73（73 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8QO9 Cryo-EM structure of a human spliceosomal B complex protomer Deposited 2023-09-28	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 66 PDB declaration: 71-meric	Chain s 1–73（73 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.29 Å
9R3D Cryo-EM structure of the human pre-Bact-OTS complex (whole map) Deposited 2025-05-04	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: 17-meric	Chain q 1–73（73 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.12 Å
9R8V Cryo-EM structure of the human pre-Bact-OTS complex (whole map) Deposited 2025-05-17	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 63-meric	Chain q 1–73（73 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.50 Å

11 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBL5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–93； 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	1p0r
Deposition date deposition_date	2003-04-10
Structure title title	Solution Structure of UBL5 a human Ubiquitin-Like Protein
Keywords keywords	Ubiquitin-like fold, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	13.03 Å
Radius of gyration Rg (electron density) rg_electron	11.42 Å
Forward intensity I(0) i0	1561390.00
Molecular weight molecular_weight	8549.0 kDa
Excluded volume excluded_volume	10801 Å³
Envelope volume envelope_volume	11896 Å³
Hydration-shell volume shell_volume	8996 Å³
Envelope diameter envelope_diameter	36.6 Å
Shell Rg shell_rg	16.95 Å
Envelope Rg envelope_rg	11.73 Å
Shape Rg shape_rg	11.41 Å
Total Rg total_rg	12.89 Å
Total atoms total_atoms	1213
Residues n_residues	73
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	39.8 Å
Rg (real space) rg_real	12.93 Å
Rg uncertainty (real space) rg_real_error	0.23 Å
I(0) (real space) i0_real	1.5610e+06
I(0) uncertainty (real space) i0_real_error	1.7580e+04
Rg (reciprocal space) rg_reciprocal	12.93 Å
I(0) (reciprocal space) i0_reciprocal	1561000.0000
Solution quality estimate total_estimate	0.8975
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.6 Å
Skewness Skewness skewness	0.080
Kurtosis Kurtosis kurtosis	-0.338
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	352400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.991

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1p0ra_
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 (1 domains)

Domain ID domain_id	1p0rA00
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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8. Citations (1)

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Description description	ubiquitin-like 5
Molecular weight formula_weight	10732.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1213

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

fit	/app/data/saxs_computation/p0/1p0r/1p0r.fit
pddf	/app/data/pr_computation/p0/1p0r/1p0r.pr.out
profile	/app/data/saxs_computation/p0/1p0r/1p0r.dat

Solution Structure of UBL5 a human Ubiquitin-Like Protein

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

ubiquitin-like 5

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)