3von

Crystalstructure of the ubiquitin protease

Method: X-RAY DIFFRACTION

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

Ubiquitin thioesterase OTUB1

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 variant 2 × 1 （Q15819） Ubiquitin-conjugating enzyme E2 N × 1 （P61088）	Consistent with protein count
10	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin-conjugating enzyme E2 variant 2 × 1 （Q15819） Ubiquitin-conjugating enzyme E2 N × 1 （P61088）	Consistent with protein count
13	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin-conjugating enzyme E2 variant 2 × 1 （Q15819） Ubiquitin-conjugating enzyme E2 N × 1 （P61088）	Consistent with protein count
16	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin-conjugating enzyme E2 variant 2 × 1 （Q15819） Ubiquitin-conjugating enzyme E2 N × 1 （P61088）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin-conjugating enzyme E2 variant 2 × 1 （Q15819） Ubiquitin-conjugating enzyme E2 N × 1 （P61088）	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin-conjugating enzyme E2 variant 2 × 1 （Q15819） 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	OTUB1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–228； UniProt 45–271 Author chain H； PDBConstruct 2–228； UniProt 45–271 Author chain O； PDBConstruct 2–228； UniProt 45–271 Author chain V； PDBConstruct 2–228； UniProt 45–271 Author chain c； PDBConstruct 2–228； UniProt 45–271 Author chain j； PDBConstruct 2–228； UniProt 45–271

Ubiquitin-conjugating enzyme E2 variant 2

Homo sapiens

UniProt Q15819

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin thioesterase OTUB1 × 1 （Q96FW1） Ubiquitin-conjugating enzyme E2 N × 1 （P61088）	Consistent with protein count
10	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin thioesterase OTUB1 × 1 （Q96FW1） Ubiquitin-conjugating enzyme E2 N × 1 （P61088）	Consistent with protein count
11	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2 N × 1 （P61088）	Consistent with protein count
12	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2 N × 1 （P61088）	Consistent with protein count
13	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin thioesterase OTUB1 × 1 （Q96FW1） Ubiquitin-conjugating enzyme E2 N × 1 （P61088）	Consistent with protein count
14	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2 N × 1 （P61088）	Consistent with protein count
15	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2 N × 1 （P61088）	Consistent with protein count
16	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin thioesterase OTUB1 × 1 （Q96FW1） Ubiquitin-conjugating enzyme E2 N × 1 （P61088）	Consistent with protein count
17	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2 N × 1 （P61088）	Consistent with protein count
18	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2 N × 1 （P61088）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2 N × 1 （P61088）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2 N × 1 （P61088）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin thioesterase OTUB1 × 1 （Q96FW1） Ubiquitin-conjugating enzyme E2 N × 1 （P61088）	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2 N × 1 （P61088）	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2 N × 1 （P61088）	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin thioesterase OTUB1 × 1 （Q96FW1） Ubiquitin-conjugating enzyme E2 N × 1 （P61088）	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2 N × 1 （P61088）	Consistent with protein count
9	Protein heterocomplex	Heteromer	Protein 2	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	UB2V2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–138； UniProt 6–143 Author chain D； PDBConstruct 1–138； UniProt 6–143 Author chain F； PDBConstruct 1–138； UniProt 6–143 Author chain I； PDBConstruct 1–138； UniProt 6–143 Author chain K； PDBConstruct 1–138； UniProt 6–143 Author chain M； PDBConstruct 1–138； UniProt 6–143 Author chain P； PDBConstruct 1–138； UniProt 6–143 Author chain R； PDBConstruct 1–138； UniProt 6–143 Author chain T； PDBConstruct 1–138； UniProt 6–143 Author chain W； PDBConstruct 1–138； UniProt 6–143 Author chain Y； PDBConstruct 1–138； UniProt 6–143 Author chain a； PDBConstruct 1–138； UniProt 6–143 Author chain d； PDBConstruct 1–138； UniProt 6–143 Author chain f； PDBConstruct 1–138； UniProt 6–143 Author chain h； PDBConstruct 1–138； UniProt 6–143 Author chain k； PDBConstruct 1–138； UniProt 6–143 Author chain m； PDBConstruct 1–138； UniProt 6–143 Author chain o； PDBConstruct 1–138； UniProt 6–143

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 thioesterase OTUB1 × 1 （Q96FW1） Ubiquitin-conjugating enzyme E2 variant 2 × 1 （Q15819）	Consistent with protein count
10	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin thioesterase OTUB1 × 1 （Q96FW1） Ubiquitin-conjugating enzyme E2 variant 2 × 1 （Q15819）	Consistent with protein count
11	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2 variant 2 × 1 （Q15819）	Consistent with protein count
12	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2 variant 2 × 1 （Q15819）	Consistent with protein count
13	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin thioesterase OTUB1 × 1 （Q96FW1） Ubiquitin-conjugating enzyme E2 variant 2 × 1 （Q15819）	Consistent with protein count
14	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2 variant 2 × 1 （Q15819）	Consistent with protein count
15	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2 variant 2 × 1 （Q15819）	Consistent with protein count
16	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin thioesterase OTUB1 × 1 （Q96FW1） Ubiquitin-conjugating enzyme E2 variant 2 × 1 （Q15819）	Consistent with protein count
17	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2 variant 2 × 1 （Q15819）	Consistent with protein count
18	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2 variant 2 × 1 （Q15819）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2 variant 2 × 1 （Q15819）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2 variant 2 × 1 （Q15819）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin thioesterase OTUB1 × 1 （Q96FW1） Ubiquitin-conjugating enzyme E2 variant 2 × 1 （Q15819）	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2 variant 2 × 1 （Q15819）	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2 variant 2 × 1 （Q15819）	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin thioesterase OTUB1 × 1 （Q96FW1） Ubiquitin-conjugating enzyme E2 variant 2 × 1 （Q15819）	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2 variant 2 × 1 （Q15819）	Consistent with protein count
9	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-conjugating enzyme E2 variant 2 × 1 （Q15819）	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	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–148； UniProt 3–150 Author chain E； PDBConstruct 1–148； UniProt 3–150 Author chain G； PDBConstruct 1–148； UniProt 3–150 Author chain J； PDBConstruct 1–148； UniProt 3–150 Author chain L； PDBConstruct 1–148； UniProt 3–150 Author chain N； PDBConstruct 1–148； UniProt 3–150 Author chain Q； PDBConstruct 1–148； UniProt 3–150 Author chain S； PDBConstruct 1–148； UniProt 3–150 Author chain U； PDBConstruct 1–148； UniProt 3–150 Author chain X； PDBConstruct 1–148； UniProt 3–150 Author chain Z； PDBConstruct 1–148； UniProt 3–150 Author chain b； PDBConstruct 1–148； UniProt 3–150 Author chain e； PDBConstruct 1–148； UniProt 3–150 Author chain g； PDBConstruct 1–148； UniProt 3–150 Author chain i； PDBConstruct 1–148； UniProt 3–150 Author chain l； PDBConstruct 1–148； UniProt 3–150 Author chain n； PDBConstruct 1–148； UniProt 3–150 Author chain p； PDBConstruct 1–148； UniProt 3–150

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	3von
Deposition date deposition_date	2012-01-30
Structure title title	Crystalstructure of the ubiquitin protease
Keywords keywords	ubiquitin protease, HYDROLASE-LIGASE complex; HYDROLASE/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.

3von__assembly_14__model_1

Assembly 14 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3von__assembly_14__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3von__assembly_14__model_1 | P(r) · Pending

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

Rg（Guinier）	23.56 Å
Rg (electron density)	22.58 Å
Total Rg	23.46 Å
Atom count	2271
Residues	285
Excluded volume	40636 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3von__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3von__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3von__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3von__assembly_4__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3von__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3von__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3von__assembly_7__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`3von__assembly_8__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`3von__assembly_9__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`3von__assembly_10__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`3von__assembly_11__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
12	1	`3von__assembly_12__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
13	1	`3von__assembly_13__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
14	1	`3von__assembly_14__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
15	1	`3von__assembly_15__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
16	1	`3von__assembly_16__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
17	1	`3von__assembly_17__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
18	1	`3von__assembly_18__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 (3)

Entity 1 Entity 1 polymer

Description description	Ubiquitin thioesterase OTUB1
Molecular weight formula_weight	26531.8 kDa
EC 编号 ec_number	3.4.19.12
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,H,O,V,c,j
Atom count atom_count	51450

SNPLVSERLELSVLYKEYAEDDNIYQQKIKDLHKKYSYIRKTRPDGNCFYRAFGFSHLEALLDDSKELQRFKAVSAKSKEDLVSQGFTEFTIEDFHNTFMDLIEQVEKQTSVADLLASFNDQSTSDYLVVYLRLLTSGYLQRESKFFEHFIEGGRTVKEFCQQEVEPMCKESDHIHIIALAQALSVSIQVEYMDRGEGGTTNPHIFPEGSEPKVYLLYRPGHYDILYK

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-conjugating enzyme E2 variant 2
Molecular weight formula_weight	15662.9 kDa
Source method src_method	man
Copy count entity_count	18

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,I,K,M,P,R,T,W,Y,a,d,f,h,k,m,o

GVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTNYENRIYSLKVECGPKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSIKVVLQELRRLMMSKENMKLPQPPEGQTY

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 polymer

Description description	Ubiquitin-conjugating enzyme E2 N
Molecular weight formula_weight	16728.2 kDa
EC 编号 ec_number	6.3.2.19
Source method src_method	man
Copy count entity_count	18

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,E,G,J,L,N,Q,S,U,X,Z,b,e,g,i,l,n,p

GLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIETARAWTRLYAMN

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

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6. Fold Classification (SCOP + CATH) 74 domains

SCOP 2.08 (26 domains)

Domain ID domain_id	d3vona_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.0 — automated matches

Domain ID domain_id	d3vonb_
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	d3vonc_
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	d3vond_
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	d3vone_
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	d3vonf_
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	d3vong_
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	d3vonh_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.0 — automated matches

Domain ID domain_id	d3voni_
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	d3vonj_
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	d3vonk_
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	d3vonl_
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	d3vonm_
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	d3vonn_
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	d3vono_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.0 — automated matches

Domain ID domain_id	d3vonp_
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	d3vonq_
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	d3vonr_
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	d3vons_
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	d3vont_
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	d3vonu_
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	d3vonv_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.0 — automated matches

Domain ID domain_id	d3vonw_
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	d3vonx_
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	d3vony_
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	d3vonz_
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

CATH v4.4 (48 domains)

Domain ID domain_id	3vonA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	60 — Peptidase C65 Otubain, subdomain 1

Domain ID domain_id	3vonA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1300 — 3 helical TM bundles of succinate and fumarate reductases
Homologous superfamily homologous superfamily	20 — Peptidase C65 Otubain, subdomain 2

Domain ID domain_id	3vonB00
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	3vonC00
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	3vonD00
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	3vonE00
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	3vonF00
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	3vonG00
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	3vonH01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	60 — Peptidase C65 Otubain, subdomain 1

Domain ID domain_id	3vonH02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1300 — 3 helical TM bundles of succinate and fumarate reductases
Homologous superfamily homologous superfamily	20 — Peptidase C65 Otubain, subdomain 2

Domain ID domain_id	3vonI00
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	3vonJ00
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	3vonK00
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	3vonL00
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	3vonM00
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	3vonN00
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	3vonO01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	60 — Peptidase C65 Otubain, subdomain 1

Domain ID domain_id	3vonO02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1300 — 3 helical TM bundles of succinate and fumarate reductases
Homologous superfamily homologous superfamily	20 — Peptidase C65 Otubain, subdomain 2

Domain ID domain_id	3vonP00
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	3vonQ00
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	3vonR00
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	3vonS00
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	3vonT00
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	3vonU00
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	3vonV01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	60 — Peptidase C65 Otubain, subdomain 1

Domain ID domain_id	3vonV02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1300 — 3 helical TM bundles of succinate and fumarate reductases
Homologous superfamily homologous superfamily	20 — Peptidase C65 Otubain, subdomain 2

Domain ID domain_id	3vonW00
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	3vonX00
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	3vonY00
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	3vonZ00
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	3vona00
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	3vonb00
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	3vonc01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	60 — Peptidase C65 Otubain, subdomain 1

Domain ID domain_id	3vonc02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1300 — 3 helical TM bundles of succinate and fumarate reductases
Homologous superfamily homologous superfamily	20 — Peptidase C65 Otubain, subdomain 2

Domain ID domain_id	3vond00
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	3vone00
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	3vonf00
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	3vong00
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	3vonh00
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	3voni00
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	3vonj01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	60 — Peptidase C65 Otubain, subdomain 1

Domain ID domain_id	3vonj02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1300 — 3 helical TM bundles of succinate and fumarate reductases
Homologous superfamily homologous superfamily	20 — Peptidase C65 Otubain, subdomain 2

Domain ID domain_id	3vonk00
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	3vonl00
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	3vonm00
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	3vonn00
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	3vono00
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	3vonp00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

▶

Unit-cell length a length_a	102.064 Å
Unit-cell length b length_b	137.285 Å
Unit-cell length c length_c	257.109 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.03 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	36

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

Resolution resolution	3.150 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2260
R_work r_work	0.2231
R_free r_free	0.2806

Crystalstructure of the ubiquitin protease

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

Ubiquitin thioesterase OTUB1

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-conjugating enzyme E2 variant 2

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3von__assembly_14__model_1

3von__assembly_14__model_1 | I(q)

3von__assembly_14__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) 74 domains

SCOP 2.08 (26 domains)

CATH v4.4 (48 domains)

7. Citations (1)

Crystalstructure of the ubiquitin protease

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

Ubiquitin thioesterase OTUB1

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 variant 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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3von__assembly_14__model_1

3von__assembly_14__model_1 | I(q)

3von__assembly_14__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) 74 domains

SCOP 2.08 (26 domains)

CATH v4.4 (48 domains)

7. Citations (1)