2fvk

Crystal structure of dihydropyrimidinase from Saccharomyces kluyveri in complex with the substrate dihydrouracil

Method: X-RAY DIFFRACTION

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

dihydropyrimidinase

Lachancea kluyveri

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	ZINC ION × 8 DIHYDROPYRIMIDINE-2,4(1H,3H)-DIONE × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9P903_SACKL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–541； UniProt 2–542 Author chain B； PDBConstruct 1–541； UniProt 2–542 Author chain C； PDBConstruct 1–541； UniProt 2–542 Author chain D； PDBConstruct 1–541； UniProt 2–542

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	2fvk
Deposition date deposition_date	2006-01-31
Structure title title	Crystal structure of dihydropyrimidinase from Saccharomyces kluyveri in complex with the substrate dihydrouracil
Keywords keywords	beta/alpha barrel, beta sandwich, 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.

2fvk__assembly_1__model_1

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

Download this curve (.dat)

2fvk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2fvk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.10 Å
Rg (electron density)	38.33 Å
Total Rg	38.66 Å
Atom count	16634
Residues	2123
Excluded volume	296650 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2fvk__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	dihydropyrimidinase
Molecular weight formula_weight	62325.1 kDa
EC 编号 ec_number	3.5.2.2
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	17698

PIYDLIIKNGIICTASDIYAAEIAVNNGKVQLIAASIDPSLGSEVIDAEGAFITPGGIDAHVHVDEPLKLLGDVVDTMEHATRSAVAGGTTTVVAFSTQDVSKKGPSALAESVKLDVDEYSEQTLYCDYGLHLILFQIEKPSVEARELLDVQLQAAYNDYGVSSVKMFMTYPGLQISDYDIMSAMYATRKNGFTTMLHAENGDMVKWMIEALEEQGLTDAYYHGVSRPSIVEGEATNRAITLATTMDTPILFVHVSSPQAAEVIKQAQTKGLKVYAETCPQYALLSDAITRCHHHGEVESYGVGIDLSSISESPFTNPDDRFIGSKYICSPPIRPEGTQKSIWKGMNNGTFTIVGSDHCSYNYYEKTSTASKHRAFDPENNKNGEFRYIPNGLPGVCTRMPLLYDYGYLRGNLTSMMKLVEIQCTNPAKVYGMYPQKGSILPGVSDADLVIWYPDDSKKEYNSKPKLITNKLMEHNCDYTPFEGIEIKNWPRYTIVKGKIVYKEGEILKENADGKYLKRGKSFMCTPKNEWVTEWRPKYESPGDDDDKHHHHHHHHSGD

Source Source

Source organism organism	Lachancea kluyveri
NCBI taxonomy ID ncbi_taxonomy_id	4934
Host organism host_organism	Escherichia coli BL21

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	8

Entity 3 Entity 3 non-polymer

Description description	DIHYDROPYRIMIDINE-2,4(1H,3H)-DIONE
Molecular weight formula_weight	114.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1043

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2fvka1
Class class	b — All beta proteins
Fold Fold fold	b.92 — Composite domain of metallo-dependent hydrolases
Superfamily Superfamily superfamily	b.92.1 — Composite domain of metallo-dependent hydrolases
Family Family family	b.92.1.3 — Hydantoinase (dihydropyrimidinase)

Domain ID domain_id	d2fvka2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
Family Family family	c.1.9.6 — Hydantoinase (dihydropyrimidinase), catalytic domain

Domain ID domain_id	d2fvkb1
Class class	b — All beta proteins
Fold Fold fold	b.92 — Composite domain of metallo-dependent hydrolases
Superfamily Superfamily superfamily	b.92.1 — Composite domain of metallo-dependent hydrolases
Family Family family	b.92.1.3 — Hydantoinase (dihydropyrimidinase)

Domain ID domain_id	d2fvkb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
Family Family family	c.1.9.6 — Hydantoinase (dihydropyrimidinase), catalytic domain

Domain ID domain_id	d2fvkc1
Class class	b — All beta proteins
Fold Fold fold	b.92 — Composite domain of metallo-dependent hydrolases
Superfamily Superfamily superfamily	b.92.1 — Composite domain of metallo-dependent hydrolases
Family Family family	b.92.1.3 — Hydantoinase (dihydropyrimidinase)

Domain ID domain_id	d2fvkc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
Family Family family	c.1.9.6 — Hydantoinase (dihydropyrimidinase), catalytic domain

Domain ID domain_id	d2fvkd1
Class class	b — All beta proteins
Fold Fold fold	b.92 — Composite domain of metallo-dependent hydrolases
Superfamily Superfamily superfamily	b.92.1 — Composite domain of metallo-dependent hydrolases
Family Family family	b.92.1.3 — Hydantoinase (dihydropyrimidinase)

Domain ID domain_id	d2fvkd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
Family Family family	c.1.9.6 — Hydantoinase (dihydropyrimidinase), catalytic domain

CATH v4.4 (8 domains)

Domain ID domain_id	2fvkA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	40 — Urease, subunit C; domain 1
Homologous superfamily homologous superfamily	10 — Urease, subunit C, domain 1

Domain ID domain_id	2fvkA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

Domain ID domain_id	2fvkB01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	40 — Urease, subunit C; domain 1
Homologous superfamily homologous superfamily	10 — Urease, subunit C, domain 1

Domain ID domain_id	2fvkB02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

Domain ID domain_id	2fvkC01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	40 — Urease, subunit C; domain 1
Homologous superfamily homologous superfamily	10 — Urease, subunit C, domain 1

Domain ID domain_id	2fvkC02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

Domain ID domain_id	2fvkD01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	40 — Urease, subunit C; domain 1
Homologous superfamily homologous superfamily	10 — Urease, subunit C, domain 1

Domain ID domain_id	2fvkD02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

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Unit-cell length a length_a	90.130 Å
Unit-cell length b length_b	71.600 Å
Unit-cell length c length_c	161.890 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.40 °
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	2.400 Å
Low-resolution limit resolution_low	54.230 Å
R factor r_factor	0.1806
R_work r_work	0.1778
R_free r_free	0.2335

Crystal structure of dihydropyrimidinase from Saccharomyces kluyveri in complex with the substrate dihydrouracil

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

dihydropyrimidinase

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

2fvk__assembly_1__model_1

2fvk__assembly_1__model_1 | I(q)

2fvk__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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (2)

Crystal structure of dihydropyrimidinase from Saccharomyces kluyveri in complex with the substrate dihydrouracil

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

dihydropyrimidinase

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

2fvk__assembly_1__model_1

2fvk__assembly_1__model_1 | I(q)

2fvk__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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (2)