SAXSdb — 2wef

▼

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

;3'(2')\, 5'-BISPHOSPHATE NUCLEOTIDASE 1 ;

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 3 PHOSPHATE ION × 1 ADENOSINE MONOPHOSPHATE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BPNT1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–304； UniProt 6–308

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	2wef
Deposition date deposition_date	2009-03-30
Structure title title	Human 3'(2'), 5'-bisphosphate nucleotidase 1 (BPNT1) in complex with AMP, PO4 and Magnesium
Keywords keywords	HYDROLASE, SULFUR METABOLISM, STRUCTURAL GENOMICS CONSORTIUM, SGC; 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.

2wef__assembly_1__model_1

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

Download this curve (.dat)

2wef__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2wef__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.52 Å
Rg (electron density)	18.43 Å
Total Rg	19.39 Å
Atom count	2342
Residues	303
Excluded volume	41871 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2wef__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	;3'(2')\, 5'-BISPHOSPHATE NUCLEOTIDASE 1 ;
Molecular weight formula_weight	33968.9 kDa
EC 编号 ec_number	3.1.3.7
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2612

MTVLMRLVASAYSIAQKAGMIVRRVIAEGDLGIVEKTCATDLQTKADRLAQMSICSSLARKFPKLTIIGEEDLPSEEVDQELIEDSQWEEILKQPCPSQYSAIKEEDLVVWVDPLDGTKEYTEGLLDNVTVLIGIAYEGKAIAGVINQPYYNYEAGPDAVLGRTIWGVLGLGAFGFQLKEVPAGKHIITTTRSHSNKLVTDCVAAMNPDAVLRVGGAGNKIIQLIEGKASAYVFASPGCKKWDTCAPEVILHAVGGKLTDIHGNVLQYHKDVKHMNSAGVLATLRNYDYYASRVPESIKNALVPAHHHHHH

Source Source

Source organism organism	HOMO SAPIENS
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE MONOPHOSPHATE
Molecular weight formula_weight	347.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	251

▼

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2wefa_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.7 — Carbohydrate phosphatase
Superfamily Superfamily superfamily	e.7.1 — Carbohydrate phosphatase
Family Family family	e.7.1.1 — Inositol monophosphatase/fructose-1,6-bisphosphatase-like

CATH v4.4 (2 domains)

Domain ID domain_id	2wefA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	540 — Fructose-1,6-Bisphosphatase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Fructose-1,6-Bisphosphatase, subunit A, domain 1

Domain ID domain_id	2wefA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	80 —

▶

Unit-cell length a length_a	38.980 Å
Unit-cell length b length_b	67.664 Å
Unit-cell length c length_c	100.394 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	4

Space group space_group	P 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	19.520 Å
R factor r_factor	0.1460
R_work r_work	0.1440
R_free r_free	0.1890

Human 3'(2'), 5'-bisphosphate nucleotidase 1 (BPNT1) in complex with AMP, PO4 and Magnesium

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

;3'(2')\, 5'-BISPHOSPHATE NUCLEOTIDASE 1 ;

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

2wef__assembly_1__model_1

2wef__assembly_1__model_1 | I(q)

2wef__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) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Human 3'(2'), 5'-bisphosphate nucleotidase 1 (BPNT1) in complex with AMP, PO4 and Magnesium

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

;3'(2')\, 5'-BISPHOSPHATE NUCLEOTIDASE 1 ;

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

2wef__assembly_1__model_1

2wef__assembly_1__model_1 | I(q)

2wef__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) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)