1r3n

Crystal structure of beta-alanine synthase from Saccharomyces kluyveri

Method: X-RAY DIFFRACTION

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

beta-alanine synthase

Lachancea kluyveri

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 BETA-AMINO ISOBUTYRATE × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 BETA-AMINO ISOBUTYRATE × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 BETA-AMINO ISOBUTYRATE × 2 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 BETA-AMINO ISOBUTYRATE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q96W94_SACKL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–454； UniProt 2–455 Author chain B； PDBConstruct 1–454； UniProt 2–455 Author chain C； PDBConstruct 1–454； UniProt 2–455 Author chain D； PDBConstruct 1–454； UniProt 2–455 Author chain E； PDBConstruct 1–454； UniProt 2–455 Author chain F； PDBConstruct 1–454； UniProt 2–455 Author chain G； PDBConstruct 1–454； UniProt 2–455 Author chain H； PDBConstruct 1–454； UniProt 2–455

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	1r3n
Deposition date deposition_date	2003-10-02
Structure title title	Crystal structure of beta-alanine synthase from Saccharomyces kluyveri
Keywords keywords	alpha and beta protein, di-zinc center, 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.

1r3n__assembly_2__model_1

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

Download this curve (.dat)

1r3n__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1r3n__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	36.39 Å
Rg (electron density)	36.61 Å
Total Rg	36.80 Å
Atom count	6772
Residues	875
Excluded volume	119550 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1r3n__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1r3n__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1r3n__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1r3n__assembly_4__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 (4)

Entity 1 Entity 1 polymer

Description description	beta-alanine synthase
Molecular weight formula_weight	50728.6 kDa
EC 编号 ec_number	3.5.1.6
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	27487

SKDVSSTITTVSASPDGTLNLPAAAPLSIASGRLNQTILETGSQFGGVARWGQESHEFGMRRLAGTALDGAMRDWFTNECESLGCKVKVDKIGNMFAVYPGKNGGKPTATGSHLDTQPEAGKYDGILGVLAGLEVLRTFKDNNYVPNYDVCVVVWFNEEGARFARSCTGSSVWSHDLSLEEAYGLMSVGEDKPESVYDSLKNIGYIGDTPASYKENEIDAHFELHIEQGPILEDENKAIGIVTGVQAYNWQKVTVHGVGAHAGTTPWRLRKDALLMSSKMIVAASEIAQRHNGLFTCGIIDAKPYSVNIIPGEVSFTLDFRHPSDDVLATMLKEAAAEFDRLIKINDGGALSYESETLQVSPAVNFHEVCIECVSRSAFAQFKKDQVRQIWSGAGHDSCQTAPHVPTSMIFIPSKDGLSHNYYEYSSPEEIENGFKVLLQAIINYDNYRVIRGHHHHHHHHH

Source Source

Source organism organism	Lachancea kluyveri
NCBI taxonomy ID ncbi_taxonomy_id	4934
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	16

Entity 3 Entity 3 non-polymer

Description description	BETA-AMINO ISOBUTYRATE
Molecular weight formula_weight	102.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	509

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d1r3na1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.4 — Bacterial dinuclear zinc exopeptidases

Domain ID domain_id	d1r3na2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.19 — Bacterial exopeptidase dimerisation domain
Family Family family	d.58.19.1 — Bacterial exopeptidase dimerisation domain

Domain ID domain_id	d1r3nb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.4 — Bacterial dinuclear zinc exopeptidases

Domain ID domain_id	d1r3nb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.19 — Bacterial exopeptidase dimerisation domain
Family Family family	d.58.19.1 — Bacterial exopeptidase dimerisation domain

Domain ID domain_id	d1r3nc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.4 — Bacterial dinuclear zinc exopeptidases

Domain ID domain_id	d1r3nc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.19 — Bacterial exopeptidase dimerisation domain
Family Family family	d.58.19.1 — Bacterial exopeptidase dimerisation domain

Domain ID domain_id	d1r3nd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.4 — Bacterial dinuclear zinc exopeptidases

Domain ID domain_id	d1r3nd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.19 — Bacterial exopeptidase dimerisation domain
Family Family family	d.58.19.1 — Bacterial exopeptidase dimerisation domain

Domain ID domain_id	d1r3ne1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.4 — Bacterial dinuclear zinc exopeptidases

Domain ID domain_id	d1r3ne2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.19 — Bacterial exopeptidase dimerisation domain
Family Family family	d.58.19.1 — Bacterial exopeptidase dimerisation domain

Domain ID domain_id	d1r3nf1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.4 — Bacterial dinuclear zinc exopeptidases

Domain ID domain_id	d1r3nf2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.19 — Bacterial exopeptidase dimerisation domain
Family Family family	d.58.19.1 — Bacterial exopeptidase dimerisation domain

Domain ID domain_id	d1r3ng1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.4 — Bacterial dinuclear zinc exopeptidases

Domain ID domain_id	d1r3ng2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.19 — Bacterial exopeptidase dimerisation domain
Family Family family	d.58.19.1 — Bacterial exopeptidase dimerisation domain

Domain ID domain_id	d1r3nh1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.4 — Bacterial dinuclear zinc exopeptidases

Domain ID domain_id	d1r3nh2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.19 — Bacterial exopeptidase dimerisation domain
Family Family family	d.58.19.1 — Bacterial exopeptidase dimerisation domain

CATH v4.4 (16 domains)

Domain ID domain_id	1r3nA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1r3nA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	360 —

Domain ID domain_id	1r3nB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1r3nB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	360 —

Domain ID domain_id	1r3nC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1r3nC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	360 —

Domain ID domain_id	1r3nD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1r3nD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	360 —

Domain ID domain_id	1r3nE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1r3nE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	360 —

Domain ID domain_id	1r3nF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1r3nF02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	360 —

Domain ID domain_id	1r3nG01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1r3nG02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	360 —

Domain ID domain_id	1r3nH01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1r3nH02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	360 —

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Unit-cell length a length_a	117.230 Å
Unit-cell length b length_b	77.120 Å
Unit-cell length c length_c	225.520 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.05 °
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	2.700 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.2112
R_work r_work	0.2084
R_free r_free	0.2658

Crystal structure of beta-alanine synthase from Saccharomyces kluyveri

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

beta-alanine synthase

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

1r3n__assembly_2__model_1

1r3n__assembly_2__model_1 | I(q)

1r3n__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (2)

Crystal structure of beta-alanine synthase from Saccharomyces kluyveri

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

beta-alanine synthase

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

1r3n__assembly_2__model_1

1r3n__assembly_2__model_1 | I(q)

1r3n__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (2)