2yaz

The Crystal Structure of Leishmania major dUTPase in complex dUMP

Method: X-RAY DIFFRACTION

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

DUTPASE

LEISHMANIA MAJOR

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	;2'-DEOXYURIDINE 5'-MONOPHOSPHATE ; × 2 SULFATE ION × 2 MAGNESIUM ION × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	;2'-DEOXYURIDINE 5'-MONOPHOSPHATE ; × 2 SULFATE ION × 2 MAGNESIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O15826_LEIMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–271； UniProt 1–268 Author chain B； PDBConstruct 4–271； UniProt 1–268 Author chain D； PDBConstruct 4–271； UniProt 1–268 Author chain E； PDBConstruct 4–271； UniProt 1–268

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	2yaz
Deposition date deposition_date	2011-02-25
Structure title title	The Crystal Structure of Leishmania major dUTPase in complex dUMP
Keywords keywords	HYDROLASE, LEISHMANIASIS; 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.

2yaz__assembly_1__model_1

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

Download this curve (.dat)

2yaz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2yaz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.04 Å
Rg (electron density)	24.01 Å
Total Rg	24.83 Å
Atom count	4055
Residues	520
Excluded volume	71688 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2yaz__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2yaz__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 (5)

Entity 1 Entity 1 polymer

Description description	DUTPASE
Molecular weight formula_weight	30609.8 kDa
EC 编号 ec_number	3.6.1.23
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,E
Atom count atom_count	8117

GPAMKRARSANIPGAILHSLAELQDGLNAMIDPSWRAVRSLDNWALAITMESTELLDSYPWKWWKNLNATPDLANVRIELVDIFHFSLSGAMQMRSTPDDEIPAASLKPLKEVMTTFLPAKECTSDPYGFVFFPLTDTQNAIASFRNIIQLANAYRFDVIIECIIYAAEDLGFNLVAYYIAKHTLNCIRQLSGYKDGSYVKVNNGVEDNSLLHNCIKDVSLDEVLDADKYVQAWNSIMANVYEAFQIKESDRKDAERWFALAKENRLAIKA

Source Source

Source organism organism	LEISHMANIA MAJOR
NCBI taxonomy ID ncbi_taxonomy_id	5664
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	;2'-DEOXYURIDINE 5'-MONOPHOSPHATE ;
Molecular weight formula_weight	308.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	35

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2yaza_
Class class	a — All alpha proteins
Fold Fold fold	a.204 — all-alpha NTP pyrophosphatases
Superfamily Superfamily superfamily	a.204.1 — all-alpha NTP pyrophosphatases
Family Family family	a.204.1.0 — automated matches

Domain ID domain_id	d2yazb_
Class class	a — All alpha proteins
Fold Fold fold	a.204 — all-alpha NTP pyrophosphatases
Superfamily Superfamily superfamily	a.204.1 — all-alpha NTP pyrophosphatases
Family Family family	a.204.1.0 — automated matches

Domain ID domain_id	d2yazd_
Class class	a — All alpha proteins
Fold Fold fold	a.204 — all-alpha NTP pyrophosphatases
Superfamily Superfamily superfamily	a.204.1 — all-alpha NTP pyrophosphatases
Family Family family	a.204.1.0 — automated matches

Domain ID domain_id	d2yaze_
Class class	a — All alpha proteins
Fold Fold fold	a.204 — all-alpha NTP pyrophosphatases
Superfamily Superfamily superfamily	a.204.1 — all-alpha NTP pyrophosphatases
Family Family family	a.204.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	2yazA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1680 — all-alpha NTP pyrophosphatases
Homologous superfamily homologous superfamily	10 — Type II deoxyuridine triphosphatase

Domain ID domain_id	2yazA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1670 — all-alpha NTP pyrophosphatase
Homologous superfamily homologous superfamily	10 — Type II deoxyuridine triphosphatase

Domain ID domain_id	2yazB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1680 — all-alpha NTP pyrophosphatases
Homologous superfamily homologous superfamily	10 — Type II deoxyuridine triphosphatase

Domain ID domain_id	2yazB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1670 — all-alpha NTP pyrophosphatase
Homologous superfamily homologous superfamily	10 — Type II deoxyuridine triphosphatase

Domain ID domain_id	2yazD01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1680 — all-alpha NTP pyrophosphatases
Homologous superfamily homologous superfamily	10 — Type II deoxyuridine triphosphatase

Domain ID domain_id	2yazD02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1670 — all-alpha NTP pyrophosphatase
Homologous superfamily homologous superfamily	10 — Type II deoxyuridine triphosphatase

Domain ID domain_id	2yazE01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1680 — all-alpha NTP pyrophosphatases
Homologous superfamily homologous superfamily	10 — Type II deoxyuridine triphosphatase

Domain ID domain_id	2yazE02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1670 — all-alpha NTP pyrophosphatase
Homologous superfamily homologous superfamily	10 — Type II deoxyuridine triphosphatase

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Unit-cell length a length_a	109.110 Å
Unit-cell length b length_b	109.110 Å
Unit-cell length c length_c	309.311 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	103.100 Å
R factor r_factor	0.2038
R_work r_work	0.2027
R_free r_free	0.2253

The Crystal Structure of Leishmania major dUTPase in complex dUMP

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

DUTPASE

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

2yaz__assembly_1__model_1

2yaz__assembly_1__model_1 | I(q)

2yaz__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

The Crystal Structure of Leishmania major dUTPase in complex dUMP

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

DUTPASE

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

2yaz__assembly_1__model_1

2yaz__assembly_1__model_1 | I(q)

2yaz__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)