3rzu

The Crystal Structure of the Catalytic Domain of AMSH

Method: X-RAY DIFFRACTION

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

STAM-binding protein

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 2 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ZINC ION × 2 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ZINC ION × 2 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	ZINC ION × 2 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	ZINC ION × 2 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	ZINC ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	STABP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–187； UniProt 243–424 Author chain B； PDBConstruct 6–187； UniProt 243–424 Author chain C； PDBConstruct 6–187； UniProt 243–424 Author chain D； PDBConstruct 6–187； UniProt 243–424 Author chain E； PDBConstruct 6–187； UniProt 243–424 Author chain F； PDBConstruct 6–187； UniProt 243–424 Author chain G； PDBConstruct 6–187； UniProt 243–424

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	3rzu
Deposition date deposition_date	2011-05-12
Structure title title	The Crystal Structure of the Catalytic Domain of AMSH
Keywords keywords	Ubiquitin Hydrolase, STAM, Endosome-associated 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.

3rzu__assembly_1__model_1

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

Download this curve (.dat)

3rzu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3rzu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.85 Å
Rg (electron density)	15.64 Å
Total Rg	16.68 Å
Atom count	1372
Residues	176
Excluded volume	24392 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3rzu__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3rzu__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3rzu__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3rzu__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3rzu__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3rzu__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3rzu__assembly_7__model_1`	monomeric （1）	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	STAM-binding protein
Molecular weight formula_weight	20616.5 kDa
EC 编号 ec_number	3.4.19.-
Source method src_method	man
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G
Atom count atom_count	9740

GPLGSSNSESIPTIDGLRHVVVPGRLCPQFLQLASANTARGVETCGILCGKLMRNEFTITHVLIPKQSAGSDYCNTENEEELFLIQDQQGLITLGWIHTHPTQTAFLSSVDLHTHCSYQMMLPESVAIVCSPKFQETGFFKLTDHGLEEISSCRQKGFHPHSKDPPLFCSCSHVTVVDRAVTITDLR

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 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	173

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d3rzua_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.3 — JAB1/MPN domain
Family Family family	c.97.3.1 — JAB1/MPN domain

Domain ID domain_id	d3rzub_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.3 — JAB1/MPN domain
Family Family family	c.97.3.1 — JAB1/MPN domain

Domain ID domain_id	d3rzuc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.3 — JAB1/MPN domain
Family Family family	c.97.3.1 — JAB1/MPN domain

Domain ID domain_id	d3rzud_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.3 — JAB1/MPN domain
Family Family family	c.97.3.1 — JAB1/MPN domain

Domain ID domain_id	d3rzue_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.3 — JAB1/MPN domain
Family Family family	c.97.3.1 — JAB1/MPN domain

Domain ID domain_id	d3rzuf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.3 — JAB1/MPN domain
Family Family family	c.97.3.1 — JAB1/MPN domain

Domain ID domain_id	d3rzug_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.3 — JAB1/MPN domain
Family Family family	c.97.3.1 — JAB1/MPN domain

CATH v4.4 (7 domains)

Domain ID domain_id	3rzuA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

Domain ID domain_id	3rzuB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

Domain ID domain_id	3rzuC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

Domain ID domain_id	3rzuD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

Domain ID domain_id	3rzuE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

Domain ID domain_id	3rzuF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

Domain ID domain_id	3rzuG00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

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Unit-cell length a length_a	203.491 Å
Unit-cell length b length_b	67.362 Å
Unit-cell length c length_c	113.165 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.44 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	28

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	47.152 Å
R factor r_factor	0.1947
R_work r_work	0.1929
R_free r_free	0.2290

The Crystal Structure of the Catalytic Domain of AMSH

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

STAM-binding protein

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

3rzu__assembly_1__model_1

3rzu__assembly_1__model_1 | I(q)

3rzu__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

CATH v4.4 (7 domains)

7. Citations (1)

The Crystal Structure of the Catalytic Domain of AMSH

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

STAM-binding protein

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

3rzu__assembly_1__model_1

3rzu__assembly_1__model_1 | I(q)

3rzu__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

CATH v4.4 (7 domains)

7. Citations (1)