SAXSdb — 6d6i

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

Ubiquitin-conjugating enzyme E2 variant 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin-conjugating enzyme E2 N × 1 （P61088） Ubv.V1.1 × 1 （Q96H31）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin-conjugating enzyme E2 N × 1 （P61088） Ubv.V1.1 × 1 （Q96H31）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UB2V1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–143； UniProt 8–147 Author chain D； PDBConstruct 4–143； UniProt 8–147

Ubiquitin-conjugating enzyme E2 N

Homo sapiens

UniProt P61088

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin-conjugating enzyme E2 variant 1 × 1 （Q13404） Ubv.V1.1 × 1 （Q96H31）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin-conjugating enzyme E2 variant 1 × 1 （Q13404） Ubv.V1.1 × 1 （Q96H31）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBE2N_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 6–155； UniProt 3–152 Author chain E； PDBConstruct 6–155； UniProt 3–152

Ubv.V1.1

Homo sapiens

UniProt Q96H31

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin-conjugating enzyme E2 variant 1 × 1 （Q13404） Ubiquitin-conjugating enzyme E2 N × 1 （P61088）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin-conjugating enzyme E2 variant 1 × 1 （Q13404） Ubiquitin-conjugating enzyme E2 N × 1 （P61088）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q96H31_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 13–88； UniProt 14–89 Author chain F； PDBConstruct 13–88； UniProt 14–89

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	6d6i
Deposition date deposition_date	2018-04-21
Structure title title	Ube2V1 in complex with ubiquitin variant Ubv.V1.1 and Ube2N/Ubc13
Keywords keywords	Ubiquitin, Ubiquitin conjugating enzyme, Ubiquitin variant, Ube2V1, TRANSFERASE; TRANSFERASE
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.

6d6i__assembly_1__model_1

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

Download this curve (.dat)

6d6i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6d6i__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.44 Å
Rg (electron density)	22.41 Å
Total Rg	23.25 Å
Atom count	4906
Residues	348
Excluded volume	45282 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6d6i__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6d6i__assembly_2__model_1`	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 (3)

Entity 1 Entity 1 polymer

Description description	Ubiquitin-conjugating enzyme E2 variant 1
Molecular weight formula_weight	16138.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	9861

GSTGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTIYENRIYSLKIECGPKYPEAPPFVRFVTKINMNGVNSSNGVVDPRAISVLAKWQNSYSIKVVLQELRRLMMSKENMKLPQPPEGQCYSN

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Ubiquitin-conjugating enzyme E2 N
Molecular weight formula_weight	17359.0 kDa
EC 编号 ec_number	2.3.2.23
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GAMGSGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIETARAWTRLYAMNNI

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Ubv.V1.1
Molecular weight formula_weight	10044.3 kDa
Mutation mutation	Q62H, K63W, H68L, V70W, L71W, R74L, G75I, G76A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GAGGDYKDDDDKMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIHWESTLLLWWRLLIA

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d6d6ia_
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	d6d6ib_
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	d6d6ic_
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	d6d6id_
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	d6d6ie_
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	d6d6if_
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

CATH v4.4 (2 domains)

Domain ID domain_id	6d6iA00
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	6d6iD00
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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Unit-cell length a length_a	91.444 Å
Unit-cell length b length_b	91.444 Å
Unit-cell length c length_c	92.446 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	trigonal

Resolution resolution	2.551 Å
Low-resolution limit resolution_low	45.722 Å
R factor r_factor	0.2651
R_work r_work	0.2635
R_free r_free	0.2963

Ube2V1 in complex with ubiquitin variant Ubv.V1.1 and Ube2N/Ubc13

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

Ubiquitin-conjugating enzyme E2 variant 1

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-conjugating enzyme E2 N

State in the Current Structure

Other States of the Same Protein in the Database

Ubv.V1.1

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

6d6i__assembly_1__model_1

6d6i__assembly_1__model_1 | I(q)

6d6i__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 (3)

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

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (6 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Ube2V1 in complex with ubiquitin variant Ubv.V1.1 and Ube2N/Ubc13

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

Ubiquitin-conjugating enzyme E2 variant 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

Ubiquitin-conjugating enzyme E2 N

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubv.V1.1

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

6d6i__assembly_1__model_1

6d6i__assembly_1__model_1 | I(q)

6d6i__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 (3)

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

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (6 domains)

CATH v4.4 (2 domains)

7. Citations (1)