SAXSdb — 6zhu

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

Ubiquitin-conjugating enzyme E2-34 kDa

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-activating enzyme E1 1 × 1 （P22515） ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-activating enzyme E1 1 × 1 （P22515） ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-activating enzyme E1 1 × 1 （P22515） ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-activating enzyme E1 1 × 1 （P22515） ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBC3_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–295； UniProt 1–295 Author chain D； PDBConstruct 1–295； UniProt 1–295 Author chain F； PDBConstruct 1–295； UniProt 1–295 Author chain H； PDBConstruct 1–295； UniProt 1–295

Ubiquitin-activating enzyme E1 1

Saccharomyces cerevisiae

UniProt P22515

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2-34 kDa × 1 （P14682） ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2-34 kDa × 1 （P14682） ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2-34 kDa × 1 （P14682） ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2-34 kDa × 1 （P14682） ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBA1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–1024； UniProt 1–1024 Author chain C； PDBConstruct 1–1024； UniProt 1–1024 Author chain E； PDBConstruct 1–1024； UniProt 1–1024 Author chain G； PDBConstruct 1–1024； UniProt 1–1024

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	6zhu
Deposition date deposition_date	2020-06-23
Structure title title	Yeast Uba1 in complex with Ubc3 and ATP
Keywords keywords	Ubiquitin, E1, Ubc3, Cdc34, 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.

6zhu__assembly_1__model_1

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

Download this curve (.dat)

6zhu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6zhu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.58 Å
Rg (electron density)	33.81 Å
Total Rg	34.39 Å
Atom count	18475
Residues	1172
Excluded volume	165760 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6zhu__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6zhu__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6zhu__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6zhu__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 (5)

Entity 1 Entity 1 polymer

Description description	Ubiquitin-conjugating enzyme E2-34 kDa
Molecular weight formula_weight	34098.8 kDa
EC 编号 ec_number	2.3.2.23
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F,D,H
Atom count atom_count	73822

MSSRKSTASSLLLRQYRELTDPKKAIPSFHIELEDDSNIFTWNIGVMVLNEDSIYHGGFFKAQMRFPEDFPFSPPQFRFTPAIYHPNVYRDGRLCISILHQSGDPMTDEPDAETWSPVQTVESVLISIVSLLEDPNINSPANVDAAVDYRKNPEQYKQRVKMEVERSKQDIPKGFIMPTSESAYISQSKLDEPESNKDMADNFWYDSDLDDDENGSVILQDDDYDDGNNHIPFEDDDVYNYNDNDDDDERIEFEDDDDDDDDSIDNDSVMDRKQPHKAEDESEDVEDVERVSKKI

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ubiquitin-activating enzyme E1 1
Molecular weight formula_weight	114393.8 kDa
EC 编号 ec_number	6.2.1.45
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,C,G

MSSNNSGLSAAGEIDESLYSRQLYVLGKEAMLKMQTSNVLILGLKGLGVEIAKNVVLAGVKSMTVFDPEPVQLADLSTQFFLTEKDIGQKRGDVTRAKLAELNAYVPVNVLDSLDDVTQLSQFQVVVATDTVSLEDKVKINEFCHSSGIRFISSETRGLFGNTFVDLGDEFTVLDPTGEEPRTGMVSDIEPDGTVTMLDDNRHGLEDGNFVRFSEVEGLDKLNDGTLFKVEVLGPFAFRIGSVKEYGEYKKGGIFTEVKVPRKISFKSLKQQLSNPEFVFSDFAKFDRAAQLHLGFQALHQFAVRHNGELPRTMNDEDANELIKLVTDLSVQQPEVLGEGVDVNEDLIKELSYQARGDIPGVVAFFGGLVAQEVLKACSGKFTPLKQFMYFDSLESLPDPKNFPRNEKTTQPVNSRYDNQIAVFGLDFQKKIANSKVFLVGSGAIGCEMLKNWALLGLGSGSDGYIVVTDNDSIEKSNLNRQFLFRPKDVGKNKSEVAAEAVCAMNPDLKGKINAKIDKVGPETEEIFNDSFWESLDFVTNALDNVDARTYVDRRCVFYRKPLLESGTLGTKGNTQVIIPRLTESYSSSRDPPEKSIPLCTLRSFPNKIDHTIAWAKSLFQGYFTDSAENVNMYLTQPNFVEQTLKQSGDVKGVLESISDSLSSKPHNFEDCIKWARLEFEKKFNHDIKQLLFNFPKDAKTSNGEPFWSGAKRAPTPLEFDIYNNDHFHFVVAGASLRAYNYGIKSDDSNSKPNVDEYKSVIDHMIIPEFTPNANLKIQVNDDDPDPNANAANGSDEIDQLVSSLPDPSTLAGFKLEPVDFEKDDDTNHHIEFITACSNCRAQNYFIETADRQKTKFIAGRIIPAIATTTSLVTGLVNLELYKLIDNKTDIEQYKNGFVNLALPFFGFSEPIASPKGEYNNKKYDKIWDRFDIKGDIKLSDLIEHFEKDEGLEITMLSYGVSLLYASFFPPKKLKERLNLPITQLVKLVTKKDIPAHVSTMILEICADDKEGEDVEVPFITIHL

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	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	9

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6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

Domain ID domain_id	6zhuA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	180 — Ubiquitin-activating enzyme E1, FCCH domain

Domain ID domain_id	6zhuA02
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	60 — Ubiquitin-activating enzyme E1, UFD domain

Domain ID domain_id	6zhuC01
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	60 — Ubiquitin-activating enzyme E1, UFD domain

Domain ID domain_id	6zhuE01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	180 — Ubiquitin-activating enzyme E1, FCCH domain

Domain ID domain_id	6zhuE02
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	60 — Ubiquitin-activating enzyme E1, UFD domain

Domain ID domain_id	6zhuG01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	180 — Ubiquitin-activating enzyme E1, FCCH domain

Domain ID domain_id	6zhuG02
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	60 — Ubiquitin-activating enzyme E1, UFD domain

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Unit-cell length a length_a	75.636 Å
Unit-cell length b length_b	152.408 Å
Unit-cell length c length_c	252.567 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.45 °
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	3.180 Å
Low-resolution limit resolution_low	49.810 Å
R factor r_factor	0.2192
R_work r_work	0.2170
R_free r_free	0.2627

Yeast Uba1 in complex with Ubc3 and ATP

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

Ubiquitin-conjugating enzyme E2-34 kDa

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-activating enzyme E1 1

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

6zhu__assembly_1__model_1

6zhu__assembly_1__model_1 | I(q)

6zhu__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 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

7. Citations (1)

Yeast Uba1 in complex with Ubc3 and ATP

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

Ubiquitin-conjugating enzyme E2-34 kDa

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-activating enzyme E1 1

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

6zhu__assembly_1__model_1

6zhu__assembly_1__model_1 | I(q)

6zhu__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 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

7. Citations (1)