SAXSdb — 2wpv

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

UPF0363 PROTEIN YOR164C

SACCHAROMYCES CEREVISIAE

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	UBIQUITIN-LIKE PROTEIN MDY2 × 1 （Q12285） MERCURY (II) ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	UBIQUITIN-LIKE PROTEIN MDY2 × 1 （Q12285） MERCURY (II) ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	UBIQUITIN-LIKE PROTEIN MDY2 × 1 （Q12285） MERCURY (II) ION × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	UBIQUITIN-LIKE PROTEIN MDY2 × 1 （Q12285） MERCURY (II) ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YO164_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–312； UniProt 1–312 Author chain C； PDBConstruct 1–312； UniProt 1–312 Author chain E； PDBConstruct 1–312； UniProt 1–312 Author chain G； PDBConstruct 1–312； UniProt 1–312

UBIQUITIN-LIKE PROTEIN MDY2

SACCHAROMYCES CEREVISIAE

UniProt Q12285

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	UPF0363 PROTEIN YOR164C × 1 （Q12125） MERCURY (II) ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	UPF0363 PROTEIN YOR164C × 1 （Q12125） MERCURY (II) ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	UPF0363 PROTEIN YOR164C × 1 （Q12125） MERCURY (II) ION × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	UPF0363 PROTEIN YOR164C × 1 （Q12125） MERCURY (II) ION × 1 water × 2	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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–59； UniProt 1–59 Author chain D； PDBConstruct 1–59； UniProt 1–59 Author chain F； PDBConstruct 1–59； UniProt 1–59 Author chain H； PDBConstruct 1–59； UniProt 1–59

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	2wpv
Deposition date deposition_date	2009-08-11
Structure title title	Crystal structure of S. cerevisiae Get4-Get5 complex
Keywords keywords	GOLGI-ER TRAFFICKING, TAIL-ANCHORED PROTEIN, PROTEIN BINDING, GET5, GET4; PROTEIN BINDING
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.

2wpv__assembly_1__model_1

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

Download this curve (.dat)

2wpv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2wpv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.13 Å
Rg (electron density)	24.59 Å
Total Rg	25.29 Å
Atom count	2709
Residues	329
Excluded volume	48735 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2wpv__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2wpv__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2wpv__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2wpv__assembly_4__model_1`	dimeric （2）	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 (4)

Entity 1 Entity 1 polymer

Description description	UPF0363 PROTEIN YOR164C
Molecular weight formula_weight	36320.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	12001

MVPAESNAVQAKLAKTLQRFENKIKAGDYYEAHQTLRTIANRYVRSKSYEHAIELISQGALSFLKAKQGGSGTDLIFYLLEVYDLAEVKVDDISVARLVRLIAELDPSEPNLKDVITGMNNWSIKFSEYKFGDPYLHNTIGSKLLEGDFVYEAERYFMLGTHDSMIKYVDLLWDWLCQVDDIEDSTVAEFFSRLVFNYLFISNISFAHESKDIFLERFIEKFHPKYEKIDKNGYEIVFFEDYSDLNFLQLLLITCQTKDKSYFLNLKNHYLDFSQAYKSELEFLGQEYFNIVAPKQTNFLQDMMSGFLGGSK

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	UBIQUITIN-LIKE PROTEIN MDY2
Molecular weight formula_weight	6634.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

MSTSASGPEHEFVSKFLTLATLTEPKLPKSYTKPLKDVTNLGVPLPTLKYKYKQNRAKK

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 non-polymer

Description description	MERCURY (II) ION
Molecular weight formula_weight	200.6 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1202

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	2wpvA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	2wpvB01
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	510 — Single helix bin

Domain ID domain_id	2wpvC00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	2wpvD01
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	510 — Single helix bin

Domain ID domain_id	2wpvE00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	2wpvF01
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	510 — Single helix bin

Domain ID domain_id	2wpvG00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	2wpvH01
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	510 — Single helix bin

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Unit-cell length a length_a	48.275 Å
Unit-cell length b length_b	118.770 Å
Unit-cell length c length_c	168.377 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.17 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.990 Å
Low-resolution limit resolution_low	25.590 Å
R factor r_factor	0.1750
R_work r_work	0.1750
R_free r_free	0.2060

Crystal structure of S. cerevisiae Get4-Get5 complex

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

UPF0363 PROTEIN YOR164C

State in the Current Structure

Other States of the Same Protein in the Database

UBIQUITIN-LIKE PROTEIN MDY2

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

2wpv__assembly_1__model_1

2wpv__assembly_1__model_1 | I(q)

2wpv__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of S. cerevisiae Get4-Get5 complex

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

UPF0363 PROTEIN YOR164C

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 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2wpv__assembly_1__model_1

2wpv__assembly_1__model_1 | I(q)

2wpv__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)