SAXSdb — 5hkh

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

Ubiquitin-fold modifier 1

Homo sapiens

UniProt P61960

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 2–83 Chain C； UniProt 2–83	Not recorded	ASP-ASN-GLU-TRP-GLY-ILE-GLU-LEU-VAL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium acetate, 0.01 M magnesium acetate, 30% polyethylene glycol 8000, 0.05 M sodium cacodylate, pH 8.0	Resolution 2.55 Å R-free 0.248

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 5HKH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1WXS Solution Structure of Ufm1, a ubiquitin-fold modifier Deposited 2005-02-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–85（85 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 100mM；Pressure ambient NMR sample composition 0.1mM Ufm1 U-13C,15N; 10mM phosphate buffer NA; 100mM NaCl; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
5IA7 Crystal structure of Ubiquitin fold modifier 1 (Ufm1) Deposited 2016-02-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–83（83 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate and 30% PEG 4000	Resolution 2.00 Å R-free 0.230
5IA7 Crystal structure of Ubiquitin fold modifier 1 (Ufm1) Deposited 2016-02-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–83（83 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate and 30% PEG 4000	Resolution 2.00 Å R-free 0.230
5IA8 Structure of a Ubiquitin like protein with an E1 fragment Deposited 2016-02-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–83（83 aa） Fragment：UNP residues 334-346,UNP residues 1-83	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2M Potassium phosphate dibasic and 20% PEG 3350	Resolution 2.00 Å R-free 0.236
5IA8 Structure of a Ubiquitin like protein with an E1 fragment Deposited 2016-02-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–83（83 aa） Fragment：UNP residues 334-346,UNP residues 1-83	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2M Potassium phosphate dibasic and 20% PEG 3350	Resolution 2.00 Å R-free 0.236
5IAA Crystal structure of human UBA5 in complex with UFM1 Deposited 2016-02-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–83（83 aa） Chain D 1–83（83 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；8% Tascimate, pH 7.0 and 16% PEG3350	Resolution 1.85 Å R-free 0.206
5L95 Crystal structure of human UBA5 in complex with UFM1 and AMP Deposited 2016-06-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 4–83（80 aa） Chain D 4–83（80 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1M HEPES pH7.5, 10% PEG 6000 and 5% 2-Methyl-2,4-pentanediol (MPD)	Resolution 2.10 Å R-free 0.222
6H77 E1 enzyme for ubiquitin like protein activation in complex with UBL Deposited 2018-07-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain Q 1–78（78 aa） Chain T 1–78（78 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 18	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；293.15 K；0.2 M Lithium Nitrate, 21% PEG 3350, 0.2 M Magnesium chloride hexahydrate and 3.5 % v/v Pentaerythritol ethoxylate (3/4 EO/OH)	Resolution 2.10 Å R-free 0.221
6H77 E1 enzyme for ubiquitin like protein activation in complex with UBL Deposited 2018-07-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain R 1–78（78 aa） Chain S 1–78（78 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 17 PEG DI(HYDROXYETHYL)ETHER × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；293.15 K；0.2 M Lithium Nitrate, 21% PEG 3350, 0.2 M Magnesium chloride hexahydrate and 3.5 % v/v Pentaerythritol ethoxylate (3/4 EO/OH)	Resolution 2.10 Å R-free 0.221
7W3N Crystal structure of Ufm1 fused to UFBP1 UFIM Deposited 2021-11-25	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–83（83 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；28% 2-propanol, 3% PEG 200, 0.1M MES at pH 6.0	Resolution 1.60 Å R-free 0.200
8BZR UFC1-UFM1 conjugate Deposited 2022-12-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–83（83 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；292 K；30% v/v PEG400, 0.1M Tris, 0.2M Na citrate	Resolution 1.78 Å R-free 0.226
8OHD 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (native) Deposited 2023-03-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric	Chain D 1–85（85 aa）	Not recorded	MG MAGNESIUM ION × 220 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8OJ0 60S ribosomal subunit bound to the E3-UFM1 complex - state 2 (native) Deposited 2023-03-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric	Chain D 1–85（85 aa）	Not recorded	MG MAGNESIUM ION × 220 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8OJ5 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (in-vitro reconstitution) Deposited 2023-03-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric	Chain D 1–85（85 aa）	Not recorded	MG MAGNESIUM ION × 220 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9GY4 60S ribosomal subunit in complex with E3-UFM1 ligase and RQC machinery components NEMF and LTN1 (Composite map) Deposited 2024-10-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 55-meric	Chain D 1–85（85 aa）	Not recorded	MG MAGNESIUM ION × 219 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å

12 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UFM1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–86； UniProt 2–83 Author chain C； PDBConstruct 5–86； UniProt 2–83

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	5hkh
Deposition date deposition_date	2016-01-14
Structure title title	Crystal structure of Ufm1 in complex with UBA5
Keywords keywords	signaling protein; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	19.52 Å
Radius of gyration Rg (electron density) rg_electron	18.72 Å
Forward intensity I(0) i0	5958150.00
Molecular weight molecular_weight	18633.0 kDa
Excluded volume excluded_volume	23747 Å³
Envelope volume envelope_volume	28579 Å³
Hydration-shell volume shell_volume	13779 Å³
Envelope diameter envelope_diameter	67.7 Å
Shell Rg shell_rg	23.51 Å
Envelope Rg envelope_rg	19.13 Å
Shape Rg shape_rg	18.69 Å
Total Rg total_rg	19.66 Å
Total atoms total_atoms	1317
Residues n_residues	174
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	68.6 Å
Rg (real space) rg_real	19.66 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	5.9580e+06
I(0) uncertainty (real space) i0_real_error	7.6220e+04
Rg (reciprocal space) rg_reciprocal	19.64 Å
I(0) (reciprocal space) i0_reciprocal	5958000.0000
Solution quality estimate total_estimate	0.8233
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.4 Å
Skewness Skewness skewness	0.496
Kurtosis Kurtosis kurtosis	-0.290
Angular range angular_range	— – 0.4050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1794000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.657; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.727; Smooth: 1.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Ubiquitin-fold modifier 1
Molecular weight formula_weight	9195.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	1342

GAMESKVSFKITLTSDPRLPYKVLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAGNVFLKHGSELRIIPRDRVG

来源 Source

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

Entity 2 Entity 2 polymer

Description description	ASP-ASN-GLU-TRP-GLY-ILE-GLU-LEU-VAL
Molecular weight formula_weight	1074.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DNEWGIELV

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	25

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5hkhA00
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	5hkhC00
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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Unit-cell length a length_a	82.656 Å
Unit-cell length b length_b	82.656 Å
Unit-cell length c length_c	62.027 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	46.877 Å
R factor r_factor	0.1984
R_work r_work	0.1931
R_free r_free	0.2476

fit	/app/data/saxs_computation/hk/5hkh/5hkh.fit
pddf	/app/data/pr_computation/hk/5hkh/5hkh.pr.out
profile	/app/data/saxs_computation/hk/5hkh/5hkh.dat

Crystal structure of Ufm1 in complex with UBA5

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

Ubiquitin-fold modifier 1

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

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)