SAXSdb — 2lxc

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

Ubiquitin-like protein MDY2

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Small glutamine-rich tetratricopeptide repeat-containing protein 2 × 2 （Q12118）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MDY2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–79； UniProt 74–151

Small glutamine-rich tetratricopeptide repeat-containing protein 2

Saccharomyces cerevisiae

UniProt Q12118

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin-like protein MDY2 × 1 （Q12285）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SGT2_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–74； UniProt 2–72 Author chain C； PDBConstruct 4–74； UniProt 2–72

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	2lxc
Deposition date deposition_date	2012-08-19
Structure title title	Solution structure of the complex between the Sgt2 homodimerization domain and the Get5 UBL domain
Keywords keywords	ubiquitin-like domain, protein-protein interaction, four-helix bundle, GET pathway, PROTEIN BINDING-PROTEIN BINDING complex; PROTEIN BINDING/PROTEIN BINDING
Experimental Method method	SOLUTION NMR

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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.

2lxc__assembly_1__model_10

Assembly 1 · Model 10 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2lxc__assembly_1__model_10 | I(q)

100 plotted points; both axes use logarithmic scales.

2lxc__assembly_1__model_10 | P(r) · Pending

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

Rg（Guinier）	19.42 Å
Rg (electron density)	18.40 Å
Total Rg	19.31 Å
Atom count	3521
Residues	229
Excluded volume	31340 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2lxc__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	2	`2lxc__assembly_1__model_2`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	3	`2lxc__assembly_1__model_3`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	4	`2lxc__assembly_1__model_4`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	5	`2lxc__assembly_1__model_5`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	6	`2lxc__assembly_1__model_6`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	7	`2lxc__assembly_1__model_7`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	8	`2lxc__assembly_1__model_8`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	9	`2lxc__assembly_1__model_9`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	10	`2lxc__assembly_1__model_10`	trimeric （3）	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 (2)

Entity 1 Entity 1 polymer

Description description	Ubiquitin-like protein MDY2
Molecular weight formula_weight	9170.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	35210

MVHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKPNLE

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Small glutamine-rich tetratricopeptide repeat-containing protein 2
Molecular weight formula_weight	7889.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SVDSASKEEIAALIVNYFSSIVEKKEISEDGADSLNVAMDCISEAFGFEREAVSGILGKSEFKGQHLADILNSA

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2lxca1
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.15.1.0 — automated matches

Domain ID domain_id	d2lxca2
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 (3 domains)

Domain ID domain_id	2lxcA00
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	2lxcB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	420 — Immunoglobulin FC, subunit C

Domain ID domain_id	2lxcC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	420 — Immunoglobulin FC, subunit C

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Solution structure of the complex between the Sgt2 homodimerization domain and the Get5 UBL domain

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

Ubiquitin-like protein MDY2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Small glutamine-rich tetratricopeptide repeat-containing protein 2

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

2lxc__assembly_1__model_10

2lxc__assembly_1__model_10 | I(q)

2lxc__assembly_1__model_10 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)