SAXSdb — 2vl1

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

BETA-ALANINE SYNTHASE

SACCHAROMYCES KLUYVERI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	GLYCINE × 6 ZINC ION × 3 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	GLYCINE × 10 ZINC ION × 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

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	2vl1
Deposition date deposition_date	2008-01-07
Structure title title	Crystal structure of beta-alanine synthase from Saccharomyces kluyveri in complex with a gly-gly peptide
Keywords keywords	HYDROLASE, DI-ZINC CENTER, AMIDOHYDROLASE, ALPHA AND BETA PROTEIN, COMPLEX WITH GLYCINE-GLYCINE; 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.

2vl1__assembly_2__model_1

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

Download this curve (.dat)

2vl1__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vl1__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	33.84 Å
Rg (electron density)	33.88 Å
Total Rg	34.16 Å
Atom count	6738
Residues	863
Excluded volume	118790 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vl1__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2vl1__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 (4)

Entity 1 Entity 1 polymer

Description description	BETA-ALANINE SYNTHASE
Molecular weight formula_weight	52006.8 kDa
EC 编号 ec_number	3.5.1.6
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	14580

SKDVSSTITTVSASPDGTLNLPAAAPLSIASGRLNQTILETGSQFGGVARWGQESHEFGMRRLAGTALDGAMRDWFTNECESLGCKVKVDKIGNMFAVYPGKNGGKPTATGSHLDTQPEAGKYDGILGVLAGLEVLRTFKDNNYVPNYDVCVVVWFNEEGARFARSCTGSSVWSHDLSLEEAYGLMSVGEDKPESVYDSLKNIGYIGDTPASYKENEIDAHFELHIEQGPILEDENKAIGIVTGVQAYNWQKVTVHGVGAHAGTTPWRLRKDALLMSSKMIVAASEIAQRHNGLFTCGIIDAKPYSVNIIPGEVSFTLDFRHPSDDVLATMLKEAAAEFDRLIKINDGGALSYESETLQVSPAVNFHEVCIECVSRSAFAQFKKDQVRQIWSGAGHDSCQTAPHVPTSMIFIPSKDGLSHNYYEYSSPEEIENGFKVLLQAIINYDNYRVIRGHQFPGDDDDKHHHHHHHHSGD

Source Source

Source organism organism	SACCHAROMYCES KLUYVERI
NCBI taxonomy ID ncbi_taxonomy_id	4934
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	GLYCINE
Molecular weight formula_weight	75.1 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1028

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	2vl1A01
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	2vl1A02
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	2vl1B01
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	2vl1B02
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	2vl1C01
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	2vl1C02
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	2vl1D01
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	2vl1D02
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	49.835 Å
Unit-cell length b length_b	218.370 Å
Unit-cell length c length_c	81.499 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.85 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2050
R_work r_work	0.2020
R_free r_free	0.2630

Crystal structure of beta-alanine synthase from Saccharomyces kluyveri in complex with a gly-gly peptide

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

2vl1__assembly_2__model_1

2vl1__assembly_2__model_1 | I(q)

2vl1__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) 8 domains

CATH v4.4 (8 domains)

7. Citations (4)

Crystal structure of beta-alanine synthase from Saccharomyces kluyveri in complex with a gly-gly peptide

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

2vl1__assembly_2__model_1

2vl1__assembly_2__model_1 | I(q)

2vl1__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) 8 domains

CATH v4.4 (8 domains)

7. Citations (4)