3o4g

Structure and Catalysis of Acylaminoacyl Peptidase

Method: X-RAY DIFFRACTION

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

Acylamino-acid-releasing enzyme

Aeropyrum pernix

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 3 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	APEH_AERPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–582； UniProt 1–582 Author chain B； PDBConstruct 1–582； UniProt 1–582 Author chain C； PDBConstruct 1–582； UniProt 1–582 Author chain D； PDBConstruct 1–582； UniProt 1–582

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	3o4g
Deposition date deposition_date	2010-07-27
Structure title title	Structure and Catalysis of Acylaminoacyl Peptidase
Keywords keywords	alpha/beta hydrolase fold, beta propeller, hydrolase, oligopeptidase, size selectivity; 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.

3o4g__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3o4g__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3o4g__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	35.73 Å
Rg (electron density)	35.28 Å
Total Rg	35.64 Å
Atom count	8584
Residues	1152
Excluded volume	152480 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3o4g__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3o4g__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 (3)

Entity 1 Entity 1 polymer

Description description	Acylamino-acid-releasing enzyme
Molecular weight formula_weight	63108.6 kDa
EC 编号 ec_number	3.4.19.1
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	17523

MRIIMPVEFSRIVRDVERLIAVEKYSLQGVVDGDKLLVVGFSEGSVNAYLYDGGETVKLNREPINSVLDPHYGVGRVILVRDVSKGAEQHALFKVNTSRPGEEQRLEAVKPMRILSGVDTGEAVVFTGATEDRVALYALDGGGLRELARLPGFGFVSDIRGDLIAGLGFFGGGRVSLFTSNLSSGGLRVFDSGEGSFSSASISPGMKVTAGLETAREARLVTVDPRDGSVEDLELPSKDFSSYRPTAITWLGYLPDGRLAVVARREGRSAVFIDGERVEAPQGNHGRVVLWRGKLVTSHTSLSTPPRIVSLPSGEPLLEGGLPEDLRRSIAGSRLVWVESFDGSRVPTYVLESGRAPTPGPTVVLVHGGPFAEDSDSWDTFAASLAAAGFHVVMPNYRGSTGYGEEWRLKIIGDPCGGELEDVSAAARWARESGLASELYIMGYSYGGYMTLCALTMKPGLFKAGVAGASVVDWEEMYELSDAAFRNFIEQLTGGSREIMRSRSPINHVDRIKEPLALIHPQNDSRTPLKPLLRLMGELLARGKTFEAHIIPDAGHAINTMEDAVKILLPAVFFLATQRERR

Source Source

Source organism organism	Aeropyrum pernix
NCBI taxonomy ID ncbi_taxonomy_id	56636
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	340

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3o4ga1
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.7 — Peptidase/esterase 'gauge' domain
Family Family family	b.69.7.2 — Acylamino-acid-releasing enzyme, N-terminal donain

Domain ID domain_id	d3o4ga2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.33 — Acylamino-acid-releasing enzyme, C-terminal donain

Domain ID domain_id	d3o4gb1
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.7 — Peptidase/esterase 'gauge' domain
Family Family family	b.69.7.2 — Acylamino-acid-releasing enzyme, N-terminal donain

Domain ID domain_id	d3o4gb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.33 — Acylamino-acid-releasing enzyme, C-terminal donain

Domain ID domain_id	d3o4gc1
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.7 — Peptidase/esterase 'gauge' domain
Family Family family	b.69.7.2 — Acylamino-acid-releasing enzyme, N-terminal donain

Domain ID domain_id	d3o4gc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.33 — Acylamino-acid-releasing enzyme, C-terminal donain

Domain ID domain_id	d3o4gd1
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.7 — Peptidase/esterase 'gauge' domain
Family Family family	b.69.7.2 — Acylamino-acid-releasing enzyme, N-terminal donain

Domain ID domain_id	d3o4gd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.33 — Acylamino-acid-releasing enzyme, C-terminal donain

CATH v4.4 (8 domains)

Domain ID domain_id	3o4gA01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	150 — Peptidase/esterase 'gauge' domain

Domain ID domain_id	3o4gA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3o4gB01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	150 — Peptidase/esterase 'gauge' domain

Domain ID domain_id	3o4gB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3o4gC01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	150 — Peptidase/esterase 'gauge' domain

Domain ID domain_id	3o4gC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3o4gD01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	150 — Peptidase/esterase 'gauge' domain

Domain ID domain_id	3o4gD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

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Unit-cell length a length_a	71.212 Å
Unit-cell length b length_b	97.016 Å
Unit-cell length c length_c	109.494 Å
Unit-cell angle α angle_alpha	89.01 °
Unit-cell angle β angle_beta	109.20 °
Unit-cell angle γ angle_gamma	100.21 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	19.640 Å
R factor r_factor	0.2175
R_work r_work	0.2152
R_free r_free	0.2617

Structure and Catalysis of Acylaminoacyl Peptidase

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

Acylamino-acid-releasing enzyme

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

3o4g__assembly_2__model_1

3o4g__assembly_2__model_1 | I(q)

3o4g__assembly_2__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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Structure and Catalysis of Acylaminoacyl Peptidase

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

Acylamino-acid-releasing enzyme

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

3o4g__assembly_2__model_1

3o4g__assembly_2__model_1 | I(q)

3o4g__assembly_2__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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)