SAXSdb — 4bri

▼

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

ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I

LEGIONELLA PNEUMOPHILA

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]uridine × 2 MAGNESIUM ION × 2 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 CHLORIDE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5ZUA2_LEGPH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–360； UniProt 35–393 Author chain B； PDBConstruct 2–360； UniProt 35–393

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4bri
Deposition date deposition_date	2013-06-04
Structure title title	Legionella pneumophila NTPDase1 crystal form II (closed) in complex with MG UMPPNP
Keywords keywords	HYDROLASE, APYRASE, ATPASE, ADPASE, CD39, PURINERGIC SIGNALLING, DOMAIN ROTATION, TRANSITION STATE, NTPDASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

4bri__assembly_1__model_1

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

Download this curve (.dat)

4bri__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4bri__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.85 Å
Rg (electron density)	26.98 Å
Total Rg	27.64 Å
Atom count	5798
Residues	716
Excluded volume	102150 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4bri__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I
Molecular weight formula_weight	41880.6 kDa
EC 编号 ec_number	3.6.1.5
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	6489

MDTNPCEKHSCIAVIDAGSTGSRLHIYSYDTDDTNTPIHIEEIWNKKIKPGFASIQPNSVTIDAYLTMLLADAPIHNIPVYFYATAGMRLLPQSQQKKYYDELDYWFRQQSQWQLVEAKTITGNDEALFDWLAVNYKLDTLKSVQNKSVGVMDMGGASVQIVFPMPKNAEISKHNQVELNIYGQNINLYVHSFLGLGQTEMSHQFLNSPSCFANDYPLPDGESGQGNAPSCKEEVTSLMNSVHKVNQQIQPLLALNPVNEWYSIGGISNLASSQLFHFENSELTNQSLLQQGDNQICHQQWDILNGQYPDDEYLYQYCLLSSYYYALMVDGYGINPNQTIHYIPPEQNLDWTIGVVLHRALEHHHHHH

Source Source

Source organism organism	LEGIONELLA PNEUMOPHILA
NCBI taxonomy ID ncbi_taxonomy_id	446
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]uridine
Molecular weight formula_weight	483.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	543

▼

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4briA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	4briA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	150 — Exopolyphosphatase. Domain 2

Domain ID domain_id	4briB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	4briB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	150 — Exopolyphosphatase. Domain 2

▶

Unit-cell length a length_a	62.457 Å
Unit-cell length b length_b	86.411 Å
Unit-cell length c length_c	72.186 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.53 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	29.370 Å
R factor r_factor	0.1641
R_work r_work	0.1638
R_free r_free	0.1845

Legionella pneumophila NTPDase1 crystal form II (closed) in complex with MG UMPPNP

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

ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I

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

4bri__assembly_1__model_1

4bri__assembly_1__model_1 | I(q)

4bri__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Legionella pneumophila NTPDase1 crystal form II (closed) in complex with MG UMPPNP

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

ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I

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

4bri__assembly_1__model_1

4bri__assembly_1__model_1 | I(q)

4bri__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)