SAXSdb — 7p47

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

Structural maintenance of chromosomes protein 5

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	SUMO-conjugating enzyme UBC9 × 1 （P50623） E3 SUMO-protein ligase MMS21 × 1 （P38632） Ubiquitin-like protein SMT3 × 2 （Q12306） ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SMC5_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 44–84； UniProt 737–777

SUMO-conjugating enzyme UBC9

Saccharomyces cerevisiae

UniProt P50623

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Structural maintenance of chromosomes protein 5 × 1 （Q08204） E3 SUMO-protein ligase MMS21 × 1 （P38632） Ubiquitin-like protein SMT3 × 2 （Q12306） ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBC9_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–157； UniProt 1–157

E3 SUMO-protein ligase MMS21

Saccharomyces cerevisiae

UniProt P38632

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Structural maintenance of chromosomes protein 5 × 1 （Q08204） SUMO-conjugating enzyme UBC9 × 1 （P50623） Ubiquitin-like protein SMT3 × 2 （Q12306） ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NSE2_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 24–214； UniProt 27–267

Ubiquitin-like protein SMT3

Saccharomyces cerevisiae

UniProt Q12306

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Structural maintenance of chromosomes protein 5 × 1 （Q08204） SUMO-conjugating enzyme UBC9 × 1 （P50623） E3 SUMO-protein ligase MMS21 × 1 （P38632） ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SMT3_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 24–121； UniProt 1–98 Author chain E； PDBConstruct 24–121； UniProt 1–98

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	7p47
Deposition date deposition_date	2021-07-09
Structure title title	Structure of the E3 ligase Smc5/Nse2 in complex with Ubc9-SUMO thioester mimetic
Keywords keywords	SUMO E3 ligase activity, DNA repair, LIGASE; LIGASE
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.

7p47__assembly_1__model_1

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

Download this curve (.dat)

7p47__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7p47__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.87 Å
Rg (electron density)	28.29 Å
Total Rg	28.93 Å
Atom count	4561
Residues	562
Excluded volume	81128 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7p47__assembly_1__model_1`	pentameric （5）	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 (5)

Entity 1 Entity 1 polymer

Description description	Structural maintenance of chromosomes protein 5
Molecular weight formula_weight	9978.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	4561

MGTDEFLKAKEKINEIFEKLNTIRDEVIKKKNQNEYYRGRTGTRKDVSQKIKDIDDQIQQLLLKQRHLLSKMASSMKSLKNCQK

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	SUMO-conjugating enzyme UBC9
Molecular weight formula_weight	19071.6 kDa
EC 编号 ec_number	2.3.2.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MSSLCLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGVYPITVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQDLLDSPNPNSPKQEPAWRSFSRNKAEYDKKVLLQARQYSKGYHHHHHH

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	E3 SUMO-protein ligase MMS21
Molecular weight formula_weight	24117.1 kDa
EC 编号 ec_number	2.3.2.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MGSSHHHHHHSSGLVPRGSHMLEARDLSNIYQQCYKQIDETINQLVDSTSPSTIGIEEQVADITSTYKLLSTYESESNSGTATMVNNTDTLKILKVLPYIWNDPTCVIPDLQNPADEDDLQIEGGKIELTCPITCKPYEAPLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRDFVRDPIMELRCKIAKMKESQEQDKRSSQAIDVL

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Ubiquitin-like protein SMT3
Molecular weight formula_weight	13739.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MGSSHHHHHHSSGLVPRGSHMASMSDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGG

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

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Unit-cell length a length_a	71.144 Å
Unit-cell length b length_b	103.240 Å
Unit-cell length c length_c	115.616 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	3.314 Å
Low-resolution limit resolution_low	47.135 Å
R factor r_factor	0.2386
R_work r_work	0.2357
R_free r_free	0.2932

Structure of the E3 ligase Smc5/Nse2 in complex with Ubc9-SUMO thioester mimetic

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

Structural maintenance of chromosomes protein 5

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

E3 SUMO-protein ligase MMS21

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-like protein SMT3

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

7p47__assembly_1__model_1

7p47__assembly_1__model_1 | I(q)

7p47__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

7. Citations (1)

Structure of the E3 ligase Smc5/Nse2 in complex with Ubc9-SUMO thioester mimetic

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

Structural maintenance of chromosomes protein 5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

SUMO-conjugating enzyme UBC9

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

E3 SUMO-protein ligase MMS21

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-like protein SMT3

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

7p47__assembly_1__model_1

7p47__assembly_1__model_1 | I(q)

7p47__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

7. Citations (1)