SAXSdb — 3ong

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

Ubiquitin-activating enzyme E1-like

Saccharomyces cerevisiae

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 439–563	Fragment：UNP residues 439-563	SUMO-conjugating enzyme UBC9 × 1 （P50623）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；20% PEG3350, 0.1 M Bis-Tris pH 5.5, 0.2 M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.251
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 439–563	Fragment：UNP residues 439-563	SUMO-conjugating enzyme UBC9 × 1 （P50623）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；20% PEG3350, 0.1 M Bis-Tris pH 5.5, 0.2 M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.251

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 3ONG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3ONH Crystal structure of UBA2ufd-Ubc9: insights into E1-E2 interactions in Sumo pathways Deposited 2010-08-28	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 439–563（125 aa） Fragment：UNP residues 439-563	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；3M (NH4)2SO4, 1% MPD, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.60 Å R-free 0.178

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBA2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–127； UniProt 439–563 Author chain C； PDBConstruct 3–127； UniProt 439–563

SUMO-conjugating enzyme UBC9

Saccharomyces cerevisiae

UniProt P50623

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–157	Not recorded	Ubiquitin-activating enzyme E1-like × 1 （P52488）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；20% PEG3350, 0.1 M Bis-Tris pH 5.5, 0.2 M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.251
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–157	Not recorded	Ubiquitin-activating enzyme E1-like × 1 （P52488）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；20% PEG3350, 0.1 M Bis-Tris pH 5.5, 0.2 M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.251

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 3ONG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2EKE Structure of a SUMO-binding-motif mimic bound to Smt3p-Ubc9p: conservation of a noncovalent Ubiquitin-like protein-E2 complex as a platform for selective interactions within a SUMO pathway Deposited 2007-03-23	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–157（157 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；18% PEG 3350, 0.2M magnesium chloride, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.250
2EKE Structure of a SUMO-binding-motif mimic bound to Smt3p-Ubc9p: conservation of a noncovalent Ubiquitin-like protein-E2 complex as a platform for selective interactions within a SUMO pathway Deposited 2007-03-23	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–157（157 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；18% PEG 3350, 0.2M magnesium chloride, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.250
2GJD Distinct functional domains of Ubc9 dictate cell survival and resistance to genotoxic stress Deposited 2006-03-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–157（157 aa） Chain B 1–157（157 aa） Chain C 1–157（157 aa） Chain D 1–157（157 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；18% PEG 6000, 0.1M HEPES, 0.1M NaBr, 5mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.75 Å R-free 0.230
5JNE E2-SUMO-Siz1 E3-SUMO-PCNA complex Deposited 2016-04-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–157（157 aa） Fragment：unp residues 20-98	Mutation：C5S, A129K, K153R	ZN ZINC ION × 1 GOL GLYCEROL × 6 6LN ethane-1,2-dithiol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1 M Tris-HCl (pH 8.5), 5% PEG 10,000, 0.2 M NaCl, 10% glycerol, 3% dioxane	Resolution 2.85 Å R-free 0.250
5JNE E2-SUMO-Siz1 E3-SUMO-PCNA complex Deposited 2016-04-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 1–157（157 aa） Fragment：unp residues 20-98	Mutation：C5S, A129K, K153R	ZN ZINC ION × 1 GOL GLYCEROL × 4 6LN ethane-1,2-dithiol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1 M Tris-HCl (pH 8.5), 5% PEG 10,000, 0.2 M NaCl, 10% glycerol, 3% dioxane	Resolution 2.85 Å R-free 0.250
6Q83 Crystal structure of the biportin Pdr6 in complex with UBC9 Deposited 2018-12-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–157（156 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；Sodium cacodylate, magnesium chloride, ethanol	Resolution 4.53 Å R-free 0.271
7P47 Structure of the E3 ligase Smc5/Nse2 in complex with Ubc9-SUMO thioester mimetic Deposited 2021-07-09	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–157（157 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；311 K；12% PEG8000, 0.2M dimethyl-2-hydroxyethylammoniumpropane sulfonate (NDSB 211), 8% ethylene glycol, 0.1M MES pH 6.5	Resolution 3.31 Å R-free 0.293

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBC9_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–159； UniProt 1–157 Author chain D； PDBConstruct 3–159； UniProt 1–157

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	3ong
Deposition date deposition_date	2010-08-28
Structure title title	Crystal structure of UBA2ufd-Ubc9: insights into E1-E2 interactions in Sumo pathways
Keywords keywords	Ligase; LIGASE
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	30.20 Å
Radius of gyration Rg (electron density) rg_electron	29.25 Å
Forward intensity I(0) i0	58322800.00
Molecular weight molecular_weight	60529.0 kDa
Excluded volume excluded_volume	75919 Å³
Envelope volume envelope_volume	98205 Å³
Hydration-shell volume shell_volume	28535 Å³
Envelope diameter envelope_diameter	108.3 Å
Shell Rg shell_rg	35.62 Å
Envelope Rg envelope_rg	29.02 Å
Shape Rg shape_rg	29.27 Å
Total Rg total_rg	29.81 Å
Total atoms total_atoms	4267
Residues n_residues	542
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	104.1 Å
Rg (real space) rg_real	30.19 Å
Rg uncertainty (real space) rg_real_error	1.03 Å
I(0) (real space) i0_real	5.8320e+07
I(0) uncertainty (real space) i0_real_error	9.2000e+05
Rg (reciprocal space) rg_reciprocal	30.20 Å
I(0) (reciprocal space) i0_reciprocal	58320000.0000
Solution quality estimate total_estimate	0.6868
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	42.0 Å
Skewness Skewness skewness	0.265
Kurtosis Kurtosis kurtosis	-0.408
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11710000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.831; Stabil: 1.000; Sysdev: 0.193; Positv: 1.000; Valcen: 0.918; Smooth: 0.932

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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-activating enzyme E1-like
Molecular weight formula_weight	14324.0 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	4305

GSSKVCRGVIKLSSDCLNKMKLSDFVVLIREKYSYPQDISLLDASNQRLLFDYDFEDLNDRTLSEINLGNGSIILFSDEEGDTMIRKAIELFLDVDDELPCNTCSLPDVEVPLIKANNSPSKNEEEE

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast,lager beer yeast,yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	SUMO-conjugating enzyme UBC9
Molecular weight formula_weight	18080.6 kDa
EC 编号 ec_number	6.3.2.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GSMSSLCLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGVYPITVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQDLLDSPNPNSPAQEPAWRSFSRNKAEYDKKVLLQAKQYSK

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast,lager beer yeast,yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 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	38

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3ongb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.1 — UBC-related

Domain ID domain_id	d3ongb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3ongd1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.1 — UBC-related

Domain ID domain_id	d3ongd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	3ongA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	290 — Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A
Homologous superfamily homologous superfamily	20 — Ubiquitin-like 2 activating enzyme e1b. Chain: B, domain 3

Domain ID domain_id	3ongB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

Domain ID domain_id	3ongC01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	290 — Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A
Homologous superfamily homologous superfamily	20 — Ubiquitin-like 2 activating enzyme e1b. Chain: B, domain 3

Domain ID domain_id	3ongD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

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8. Citations (1)

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Unit-cell length a length_a	38.465 Å
Unit-cell length b length_b	134.038 Å
Unit-cell length c length_c	62.012 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.44 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	38.350 Å
R factor r_factor	0.2242
R_work r_work	0.2228
R_free r_free	0.2510

fit	/app/data/saxs_computation/on/3ong/3ong.fit
pddf	/app/data/pr_computation/on/3ong/3ong.pr.out
profile	/app/data/saxs_computation/on/3ong/3ong.dat

Crystal structure of UBA2ufd-Ubc9: insights into E1-E2 interactions in Sumo pathways

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

Ubiquitin-activating enzyme E1-like

State in the Current Structure

Other States of the Same Protein in the Database

SUMO-conjugating enzyme UBC9

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

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)