2n2k

Ensemble structure of the closed state of Lys63-linked diubiquitin in the absence of a ligand

Method: SOLUTION NMR

▼

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

ubiquitin

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBC_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–76； UniProt 1–76 Author chain B； PDBConstruct 1–71； UniProt 1–71

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2n2k
Deposition date deposition_date	2015-05-10
Structure title title	Ensemble structure of the closed state of Lys63-linked diubiquitin in the absence of a ligand
Keywords keywords	polyubiquitin, ensemble structure, protein dynamics, ubiquitin signaling, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	SOLUTION NMR

▼

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.

2n2k__assembly_1__model_27

Assembly 1 · Model 27 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2n2k__assembly_1__model_27 | I(q)

100 plotted points; both axes use logarithmic scales.

2n2k__assembly_1__model_27 | P(r) · Pending

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

Rg（Guinier）	18.32 Å
Rg (electron density)	17.89 Å
Total Rg	18.46 Å
Atom count	734
Residues	147
Excluded volume	8293 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2n2k__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	2	`2n2k__assembly_1__model_2`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	3	`2n2k__assembly_1__model_3`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	4	`2n2k__assembly_1__model_4`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	5	`2n2k__assembly_1__model_5`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	6	`2n2k__assembly_1__model_6`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	7	`2n2k__assembly_1__model_7`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	8	`2n2k__assembly_1__model_8`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	9	`2n2k__assembly_1__model_9`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	10	`2n2k__assembly_1__model_10`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	11	`2n2k__assembly_1__model_11`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	12	`2n2k__assembly_1__model_12`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	13	`2n2k__assembly_1__model_13`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	14	`2n2k__assembly_1__model_14`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	15	`2n2k__assembly_1__model_15`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	16	`2n2k__assembly_1__model_16`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	17	`2n2k__assembly_1__model_17`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	18	`2n2k__assembly_1__model_18`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	19	`2n2k__assembly_1__model_19`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	20	`2n2k__assembly_1__model_20`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	21	`2n2k__assembly_1__model_21`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	22	`2n2k__assembly_1__model_22`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	23	`2n2k__assembly_1__model_23`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	24	`2n2k__assembly_1__model_24`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	25	`2n2k__assembly_1__model_25`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	26	`2n2k__assembly_1__model_26`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	27	`2n2k__assembly_1__model_27`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	28	`2n2k__assembly_1__model_28`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	29	`2n2k__assembly_1__model_29`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	30	`2n2k__assembly_1__model_30`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	31	`2n2k__assembly_1__model_31`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	32	`2n2k__assembly_1__model_32`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	33	`2n2k__assembly_1__model_33`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	34	`2n2k__assembly_1__model_34`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	35	`2n2k__assembly_1__model_35`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	36	`2n2k__assembly_1__model_36`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	37	`2n2k__assembly_1__model_37`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	38	`2n2k__assembly_1__model_38`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	39	`2n2k__assembly_1__model_39`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	40	`2n2k__assembly_1__model_40`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	41	`2n2k__assembly_1__model_41`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	42	`2n2k__assembly_1__model_42`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	43	`2n2k__assembly_1__model_43`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	44	`2n2k__assembly_1__model_44`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	45	`2n2k__assembly_1__model_45`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	46	`2n2k__assembly_1__model_46`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	47	`2n2k__assembly_1__model_47`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	48	`2n2k__assembly_1__model_48`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	49	`2n2k__assembly_1__model_49`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	50	`2n2k__assembly_1__model_50`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	51	`2n2k__assembly_1__model_51`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	52	`2n2k__assembly_1__model_52`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	53	`2n2k__assembly_1__model_53`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	54	`2n2k__assembly_1__model_54`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	55	`2n2k__assembly_1__model_55`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	56	`2n2k__assembly_1__model_56`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	57	`2n2k__assembly_1__model_57`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	58	`2n2k__assembly_1__model_58`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	59	`2n2k__assembly_1__model_59`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	60	`2n2k__assembly_1__model_60`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	61	`2n2k__assembly_1__model_61`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	62	`2n2k__assembly_1__model_62`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	63	`2n2k__assembly_1__model_63`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	64	`2n2k__assembly_1__model_64`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	65	`2n2k__assembly_1__model_65`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	66	`2n2k__assembly_1__model_66`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	67	`2n2k__assembly_1__model_67`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	68	`2n2k__assembly_1__model_68`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	69	`2n2k__assembly_1__model_69`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	70	`2n2k__assembly_1__model_70`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	ubiquitin
Molecular weight formula_weight	8539.8 kDa
Mutation mutation	N25C, K48C
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	143150

MQIFVKTLTGKTITLEVEPSDTIECVKAKIQDKEGIPPDQQRLIFAGCQLEDGRTLSDYNIQKESTLHLVLRLRGG

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

Entity 2 Entity 2 polymer

Description description	ubiquitin
Molecular weight formula_weight	8035.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL

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

Entity 3 Entity 3 non-polymer

Description description	S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate
Molecular weight formula_weight	264.4 kDa
Source method src_method	syn
Copy count entity_count	2

▼

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2n2ka_
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.15.1.1 — Ubiquitin-related

Domain ID domain_id	d2n2kb_
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.15.1.1 — Ubiquitin-related

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Ensemble structure of the closed state of Lys63-linked diubiquitin in the absence of a ligand

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

ubiquitin

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

2n2k__assembly_1__model_27

2n2k__assembly_1__model_27 | I(q)

2n2k__assembly_1__model_27 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

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 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)

Ensemble structure of the closed state of Lys63-linked diubiquitin in the absence of a ligand

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

ubiquitin

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

2n2k__assembly_1__model_27

2n2k__assembly_1__model_27 | I(q)

2n2k__assembly_1__model_27 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

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 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)