SAXSdb — 3lqs

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

D-alanine aminotransferase

Bacillus sp.

UniProt P19938

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	4-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]THIOPHENE-2-CARBOXYLIC ACID × 2 ACETIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DAAA_BACYM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–280； UniProt 2–281 Author chain B； PDBConstruct 1–280； UniProt 2–281

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	3lqs
Deposition date deposition_date	2010-02-10
Structure title title	Complex Structure of D-Amino Acid Aminotransferase and 4-amino-4,5-dihydro-thiophenecarboxylic acid (ADTA)
Keywords keywords	PLP aminotransferase, mechanism-based inhibitor, stereo-specificity, R-ADTA, Aminotransferase, Pyridoxal phosphate, Transferase; TRANSFERASE
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.

3lqs__assembly_1__model_1

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

Download this curve (.dat)

3lqs__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3lqs__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.21 Å
Rg (electron density)	25.55 Å
Total Rg	26.45 Å
Atom count	4566
Residues	560
Excluded volume	81523 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3lqs__assembly_1__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	D-alanine aminotransferase
Molecular weight formula_weight	32060.6 kDa
EC 编号 ec_number	2.6.1.21
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	5003

GYTLWNDQIVKDEEVKIDKEDRGYQFGDGVYEVVKVYNGEMFTVNEHIDRLYASAEKIRITIPYTKDKFHQLLHELVEKNELNTGHIYFQVTRGTSPRAHQFPENTVKPVIIGYTKENPRPLENLEKGVKATFVEDIRWLRCDIKSLNLLGAVLAKQEAHEKGCYEAILHRNNTVTEGSSSNVFGIKDGILYTHPANNMILKGITRDVVIACANEINMPVKEIPFTTHEALKMDELFVTSTTSEITPVIEIDGKLIRDGKVGEWTRKLQKQFETKIPKPL

Source Source

Source organism organism	Bacillus sp.
NCBI taxonomy ID ncbi_taxonomy_id	72579
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	4-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]THIOPHENE-2-CARBOXYLIC ACID
Molecular weight formula_weight	374.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	297

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3lqsa_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.17 — D-aminoacid aminotransferase-like PLP-dependent enzymes
Superfamily Superfamily superfamily	e.17.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes
Family Family family	e.17.1.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes

Domain ID domain_id	d3lqsb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.17 — D-aminoacid aminotransferase-like PLP-dependent enzymes
Superfamily Superfamily superfamily	e.17.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes
Family Family family	e.17.1.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes

CATH v4.4 (4 domains)

Domain ID domain_id	3lqsA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain

Domain ID domain_id	3lqsA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	10 — D-amino Acid Aminotransferase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — D-amino Acid Aminotransferase, subunit A, domain 2

Domain ID domain_id	3lqsB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain

Domain ID domain_id	3lqsB02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	10 — D-amino Acid Aminotransferase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — D-amino Acid Aminotransferase, subunit A, domain 2

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Unit-cell length a length_a	77.011 Å
Unit-cell length b length_b	90.728 Å
Unit-cell length c length_c	88.893 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	63.500 Å
R factor r_factor	0.1623
R_work r_work	0.1605
R_free r_free	0.1958

Complex Structure of D-Amino Acid Aminotransferase and 4-amino-4,5-dihydro-thiophenecarboxylic acid (ADTA)

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

D-alanine aminotransferase

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

3lqs__assembly_1__model_1

3lqs__assembly_1__model_1 | I(q)

3lqs__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 (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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Complex Structure of D-Amino Acid Aminotransferase and 4-amino-4,5-dihydro-thiophenecarboxylic acid (ADTA)

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

D-alanine aminotransferase

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

3lqs__assembly_1__model_1

3lqs__assembly_1__model_1 | I(q)

3lqs__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 (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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)