1ryy

Acetobacter turbidans alpha-amino acid ester hydrolase Y206A mutant

Method: X-RAY DIFFRACTION

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

alpha-amino acid ester hydrolase

Acetobacter pasteurianus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8VRK8_ACEPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–627； UniProt 41–667 Author chain B； PDBConstruct 1–627； UniProt 41–667 Author chain C； PDBConstruct 1–627； UniProt 41–667 Author chain D； PDBConstruct 1–627； UniProt 41–667 Author chain E； PDBConstruct 1–627； UniProt 41–667 Author chain F； PDBConstruct 1–627； UniProt 41–667 Author chain G； PDBConstruct 1–627； UniProt 41–667 Author chain H； PDBConstruct 1–627； UniProt 41–667

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	1ryy
Deposition date deposition_date	2003-12-23
Structure title title	Acetobacter turbidans alpha-amino acid ester hydrolase Y206A mutant
Keywords keywords	alpha/beta hydrolase fold, jellyroll fold, 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.

1ryy__assembly_1__model_1

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

Download this curve (.dat)

1ryy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ryy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.22 Å
Rg (electron density)	39.43 Å
Total Rg	39.97 Å
Atom count	19344
Residues	2448
Excluded volume	340550 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ryy__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1ryy__assembly_2__model_1`	tetrameric （4）	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 (2)

Entity 1 Entity 1 polymer

Description description	alpha-amino acid ester hydrolase
Molecular weight formula_weight	72855.4 kDa
EC 编号 ec_number	3.1.1.43
Mutation mutation	Y206A
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	39009

APAADAAQAHDPLSVQTGSDIPASVHMPTDQQRDYIKREVMVPMRDGVKLYTVIVIPKNARNAPILLTRTPYNAKGRANRVPNALTMREVLPQGDDVFVEGGYIRVFQDIRGKYGSQGDYVMTRPPHGPLNPTKTDETTDAWDTVDWLVHNVPESNGRVGMTGSSAEGFTVVMALLDPHPALKVAAPESPMVDGWMGDDWFHYGAFRQGAFDYFVSQMTARGGGNDIPRRDADDYTNFLKAGSAGSFATQAGLDQYPFWQRMHAHPAYDAFWQGQALDKILAQRKPTVPMLWEQGLWDQEDMWGAIHAWQALKDADVKAPNTLVMGPWRHSGVNYNGSTLGPLEFEGDTAHQYRRDVFRPFFDEYLKPGSASVHLPDAIIYNTGDQKWDYYRSWPSVCESNCTGGLTPLYLADGHGLSFTHPAADGADSYVSDPAHPVPFISRPFAFAQSSRWKPWLVQDQREAESRPDVVTYETEVLDEPVRVSGVPVADLFAATSGTDSDWVVKLIDVQPAMTPDDPKMGGYELPVSMDIFRGRYRKDFAKPEALQPDATLHYHFTLPAVNHVFAKGHRIMVQIQSSWFPLYDRNPQKFVPNIFDAKPADYTVATQSIHHGGKEATSILLPVVKQKLGPEQKLISEEDLNSAVDHHHHHH

Source Source

Source organism organism	Acetobacter pasteurianus
NCBI taxonomy ID ncbi_taxonomy_id	438
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	321

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6. Fold Classification (SCOP + CATH) 40 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d1ryya1
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.13 — PepX C-terminal domain-like

Domain ID domain_id	d1ryya2
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.69.1.21 — PepX catalytic domain-like

Domain ID domain_id	d1ryyb1
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.13 — PepX C-terminal domain-like

Domain ID domain_id	d1ryyb2
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.69.1.21 — PepX catalytic domain-like

Domain ID domain_id	d1ryyc1
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.13 — PepX C-terminal domain-like

Domain ID domain_id	d1ryyc2
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.69.1.21 — PepX catalytic domain-like

Domain ID domain_id	d1ryyd1
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.13 — PepX C-terminal domain-like

Domain ID domain_id	d1ryyd2
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.69.1.21 — PepX catalytic domain-like

Domain ID domain_id	d1ryye1
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.13 — PepX C-terminal domain-like

Domain ID domain_id	d1ryye2
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.69.1.21 — PepX catalytic domain-like

Domain ID domain_id	d1ryyf1
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.13 — PepX C-terminal domain-like

Domain ID domain_id	d1ryyf2
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.69.1.21 — PepX catalytic domain-like

Domain ID domain_id	d1ryyg1
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.13 — PepX C-terminal domain-like

Domain ID domain_id	d1ryyg2
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.69.1.21 — PepX catalytic domain-like

Domain ID domain_id	d1ryyh1
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.13 — PepX C-terminal domain-like

Domain ID domain_id	d1ryyh2
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.69.1.21 — PepX catalytic domain-like

CATH v4.4 (24 domains)

Domain ID domain_id	1ryyA01
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	1ryyA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3020 — alpha-amino acid ester hydrolase ( Helical cap domain)
Homologous superfamily homologous superfamily	10 — alpha-amino acid ester hydrolase ( Helical cap domain)

Domain ID domain_id	1ryyA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	1ryyB01
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	1ryyB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3020 — alpha-amino acid ester hydrolase ( Helical cap domain)
Homologous superfamily homologous superfamily	10 — alpha-amino acid ester hydrolase ( Helical cap domain)

Domain ID domain_id	1ryyB03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	1ryyC01
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	1ryyC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3020 — alpha-amino acid ester hydrolase ( Helical cap domain)
Homologous superfamily homologous superfamily	10 — alpha-amino acid ester hydrolase ( Helical cap domain)

Domain ID domain_id	1ryyC03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	1ryyD01
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	1ryyD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3020 — alpha-amino acid ester hydrolase ( Helical cap domain)
Homologous superfamily homologous superfamily	10 — alpha-amino acid ester hydrolase ( Helical cap domain)

Domain ID domain_id	1ryyD03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	1ryyE01
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	1ryyE02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3020 — alpha-amino acid ester hydrolase ( Helical cap domain)
Homologous superfamily homologous superfamily	10 — alpha-amino acid ester hydrolase ( Helical cap domain)

Domain ID domain_id	1ryyE03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	1ryyF01
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	1ryyF02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3020 — alpha-amino acid ester hydrolase ( Helical cap domain)
Homologous superfamily homologous superfamily	10 — alpha-amino acid ester hydrolase ( Helical cap domain)

Domain ID domain_id	1ryyF03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	1ryyG01
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	1ryyG02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3020 — alpha-amino acid ester hydrolase ( Helical cap domain)
Homologous superfamily homologous superfamily	10 — alpha-amino acid ester hydrolase ( Helical cap domain)

Domain ID domain_id	1ryyG03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	1ryyH01
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	1ryyH02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3020 — alpha-amino acid ester hydrolase ( Helical cap domain)
Homologous superfamily homologous superfamily	10 — alpha-amino acid ester hydrolase ( Helical cap domain)

Domain ID domain_id	1ryyH03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

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Unit-cell length a length_a	91.649 Å
Unit-cell length b length_b	177.513 Å
Unit-cell length c length_c	169.967 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.03 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2110
R_work r_work	0.2097
R_free r_free	0.2359

Acetobacter turbidans alpha-amino acid ester hydrolase Y206A mutant

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

alpha-amino acid ester hydrolase

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

1ryy__assembly_1__model_1

1ryy__assembly_1__model_1 | I(q)

1ryy__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 40 domains

SCOP 2.08 (16 domains)

CATH v4.4 (24 domains)

7. Citations (1)

Acetobacter turbidans alpha-amino acid ester hydrolase Y206A mutant

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

alpha-amino acid ester hydrolase

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

1ryy__assembly_1__model_1

1ryy__assembly_1__model_1 | I(q)

1ryy__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 40 domains

SCOP 2.08 (16 domains)

CATH v4.4 (24 domains)

7. Citations (1)