8oyp

Crystal structure of Ubiquitin specific protease 11 (USP11) in complex with a substrate mimetic

Method: X-RAY DIFFRACTION

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

Ubiquitin carboxyl-terminal hydrolase 11,Response regulator FrzS

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Polyubiquitin-B × 1 （P0CG47） CADMIUM ION × 1 CHLORIDE ION × 1 NITRATE ION × 2 PHOSPHATE ION × 1 GLYCEROL × 1 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2	Polyubiquitin-B × 1 （P0CG47） CADMIUM ION × 1 CHLORIDE ION × 1 NITRATE ION × 2 PHOSPHATE ION × 1 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBP11_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–195； UniProt 295–489 Author chain A； PDBConstruct 319–478； UniProt 778–937 Author chain B； PDBConstruct 1–195； UniProt 295–489 Author chain B； PDBConstruct 319–478； UniProt 778–937

Ubiquitin carboxyl-terminal hydrolase 11,Response regulator FrzS

Homo sapiens

UniProt Q1D4U9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Polyubiquitin-B × 1 （P0CG47） CADMIUM ION × 1 CHLORIDE ION × 1 NITRATE ION × 2 PHOSPHATE ION × 1 GLYCEROL × 1 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2	Polyubiquitin-B × 1 （P0CG47） CADMIUM ION × 1 CHLORIDE ION × 1 NITRATE ION × 2 PHOSPHATE ION × 1 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q1D4U9_MYXXD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 198–312； UniProt 3–117 Author chain B； PDBConstruct 198–312； UniProt 3–117

Polyubiquitin-B

Homo sapiens

UniProt P0CG47

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Ubiquitin carboxyl-terminal hydrolase 11,Response regulator FrzS × 1 （P51784,Q1D4U9） CADMIUM ION × 1 CHLORIDE ION × 1 NITRATE ION × 2 PHOSPHATE ION × 1 GLYCEROL × 1 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2	Ubiquitin carboxyl-terminal hydrolase 11,Response regulator FrzS × 1 （P51784,Q1D4U9） CADMIUM ION × 1 CHLORIDE ION × 1 NITRATE ION × 2 PHOSPHATE ION × 1 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBB_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–76； UniProt 1–76 Author chain D； PDBConstruct 1–76； UniProt 1–76

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	8oyp
Deposition date deposition_date	2023-05-05
Structure title title	Crystal structure of Ubiquitin specific protease 11 (USP11) in complex with a substrate mimetic
Keywords keywords	Protease, Ubiquitin, Substrate complex, Deubiquitinating enzyme, HYDROLASE; HYDROLASE
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.

8oyp__assembly_1__model_1

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

Download this curve (.dat)

8oyp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8oyp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.95 Å
Rg (electron density)	24.84 Å
Total Rg	25.70 Å
Atom count	4372
Residues	548
Excluded volume	77465 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8oyp__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8oyp__assembly_2__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 (8)

Entity 1 Entity 1 polymer

Description description	Ubiquitin carboxyl-terminal hydrolase 11,Response regulator FrzS
Molecular weight formula_weight	55166.9 kDa
EC 编号 ec_number	3.4.19.12
Mutation mutation	C318S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9397

MSEEDEDFKGQPGICGLTNLGNTSFMNSALQCLSNVPQLTEYFLNNCYLEELNFRNPLGMKGEIAEAYADLVKQAWSGHHRSIVPHVFKNKVGHFASQFLGYQQHDSQELLSFLLDGLHEDLNRVKKKEYVELCDAAGRPDQEVAQEAWQNHKRRNDSVIVDTFHGLFKSTLVCPDCGNVSVTFDPFCYLSVPLPGAKKILIVESDTALSATLRSALEGRGFTVDETTDGKGSVEQIRRDRPDLVVLAVDLSAGQNGYLICGKLKKDDDLKNVPIVIIGNPDGFAQHRALSAHADEYVAKPVDADQLVERAGALIGFPPVRLQECIELFTTVETLEKENPWYCPSCKQHQLATKKLDLWMLPEILIIHLKRFSYTKFSREKLDTLVEFPIRDLDFSEFVIQPQNESNPELYKYDLIAVSNHYGGMRDGHYTTFACNKDSGQWHYFDDNSVSPVNENQIESKAAYVLFYQRQDVARRLLEHHHHHH

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 2 Entity 2 polymer

Description description	Polyubiquitin-B
Molecular weight formula_weight	8748.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGGGG

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 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	NITRATE ION
Molecular weight formula_weight	62.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	505

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Unit-cell length a length_a	94.321 Å
Unit-cell length b length_b	186.102 Å
Unit-cell length c length_c	75.761 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.440 Å
Low-resolution limit resolution_low	48.000 Å
R factor r_factor	0.1730
R_work r_work	0.1697
R_free r_free	0.2351

Crystal structure of Ubiquitin specific protease 11 (USP11) in complex with a substrate mimetic

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

Ubiquitin carboxyl-terminal hydrolase 11,Response regulator FrzS

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin carboxyl-terminal hydrolase 11,Response regulator FrzS

State in the Current Structure

Other States of the Same Protein in the Database

Polyubiquitin-B

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

8oyp__assembly_1__model_1

8oyp__assembly_1__model_1 | I(q)

8oyp__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 (8)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

Crystal structure of Ubiquitin specific protease 11 (USP11) in complex with a substrate mimetic

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

Ubiquitin carboxyl-terminal hydrolase 11,Response regulator FrzS

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 carboxyl-terminal hydrolase 11,Response regulator FrzS

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Polyubiquitin-B

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

8oyp__assembly_1__model_1

8oyp__assembly_1__model_1 | I(q)

8oyp__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 (8)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)