1hpu

5'-NUCLEOTIDASE (CLOSED FORM), COMPLEX WITH AMPCP

Method: X-RAY DIFFRACTION

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

5'-NUCLEOTIDASE

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	USHA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–525； UniProt 26–550 Author chain B； PDBConstruct 1–525； UniProt 26–550 Author chain C； PDBConstruct 1–525； UniProt 26–550 Author chain D； PDBConstruct 1–525； UniProt 26–550

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	1hpu
Deposition date deposition_date	2000-12-13
Structure title title	5'-NUCLEOTIDASE (CLOSED FORM), COMPLEX WITH AMPCP
Keywords keywords	metalloenzyme, metallophosphatase, domain rotation, domain movement, 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.

1hpu__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1hpu__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1hpu__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	25.12 Å
Rg (electron density)	24.52 Å
Total Rg	25.32 Å
Atom count	4129
Residues	525
Excluded volume	73098 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1hpu__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1hpu__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1hpu__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1hpu__assembly_4__model_1`	monomeric （1）	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	5'-NUCLEOTIDASE
Molecular weight formula_weight	58277.6 kDa
EC 编号 ec_number	3.1.3.5, 3.6.1.45
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	17735

YEQDKTYKITVLHTNDHHGHFWRNEYGEYGLAAQKTLVDGIRKEVAAEGGSVLLLSGGDINTGVPESDLQDAEPDFRGMNLVGYDAMAIGNHEFDNPLTVLRQQEKWAKFPLLSANIYQKSTGERLFKPWALFKRQDLKIAVIGLTTDDTAKIGNPEYFTDIEFRKPADEAKLVIQELQQTEKPDIIIAATHMGHYDNGEHGSNAPGDVEMARALPAGSLAMIVGGHSQDPVCMAAENKKQVDYVPGTPCKPDQQNGIWIVQAHEWGKYVGRADFEFRNGEMKMVNYQLIPVNLKKKVTWEDGKSERVLYTPEIAENQQMISLLSPFQNKGKAQLEVKIGETNGRLEGDRDKVRFVQTNMGRLILAAQMDRTGADFAVMSGGGIRDSIEAGDISYKNVLKVQPFGNVVVYADMTGKEVIDYLTAVAQMKPDSGAYPQFANVSFVAKDGKLNDLKIKGEPVDPAKTYRMATLNFNATGGDGYPRLDNKPGYVNTGFIDAEVLKAYIQKSSPLDVSVYEPKGEVSWQ

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
Molecular weight formula_weight	425.2 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	1219

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1hpua1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.114 — 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain
Superfamily Superfamily superfamily	d.114.1 — 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain
Family Family family	d.114.1.1 — 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain

Domain ID domain_id	d1hpua2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamily	d.159.1 — Metallo-dependent phosphatases
Family Family family	d.159.1.2 — 5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain

Domain ID domain_id	d1hpub1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.114 — 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain
Superfamily Superfamily superfamily	d.114.1 — 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain
Family Family family	d.114.1.1 — 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain

Domain ID domain_id	d1hpub2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamily	d.159.1 — Metallo-dependent phosphatases
Family Family family	d.159.1.2 — 5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain

Domain ID domain_id	d1hpuc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.114 — 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain
Superfamily Superfamily superfamily	d.114.1 — 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain
Family Family family	d.114.1.1 — 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain

Domain ID domain_id	d1hpuc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamily	d.159.1 — Metallo-dependent phosphatases
Family Family family	d.159.1.2 — 5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain

Domain ID domain_id	d1hpud1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.114 — 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain
Superfamily Superfamily superfamily	d.114.1 — 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain
Family Family family	d.114.1.1 — 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain

Domain ID domain_id	d1hpud2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamily	d.159.1 — Metallo-dependent phosphatases
Family Family family	d.159.1.2 — 5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain

CATH v4.4 (8 domains)

Domain ID domain_id	1hpuA01
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily	10 — Metallo-dependent phosphatases

Domain ID domain_id	1hpuA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	780 — 5'-nucleotidase; domain 2
Homologous superfamily homologous superfamily	10 — 5'-Nucleotidase, C-terminal domain

Domain ID domain_id	1hpuB01
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily	10 — Metallo-dependent phosphatases

Domain ID domain_id	1hpuB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	780 — 5'-nucleotidase; domain 2
Homologous superfamily homologous superfamily	10 — 5'-Nucleotidase, C-terminal domain

Domain ID domain_id	1hpuC01
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily	10 — Metallo-dependent phosphatases

Domain ID domain_id	1hpuC02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	780 — 5'-nucleotidase; domain 2
Homologous superfamily homologous superfamily	10 — 5'-Nucleotidase, C-terminal domain

Domain ID domain_id	1hpuD01
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily	10 — Metallo-dependent phosphatases

Domain ID domain_id	1hpuD02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	780 — 5'-nucleotidase; domain 2
Homologous superfamily homologous superfamily	10 — 5'-Nucleotidase, C-terminal domain

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Unit-cell length a length_a	89.400 Å
Unit-cell length b length_b	89.960 Å
Unit-cell length c length_c	96.260 Å
Unit-cell angle α angle_alpha	110.79 °
Unit-cell angle β angle_beta	106.43 °
Unit-cell angle γ angle_gamma	107.76 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	28.590 Å
R factor r_factor	0.2070
R_work r_work	0.2070
R_free r_free	0.2340

5'-NUCLEOTIDASE (CLOSED FORM), COMPLEX WITH AMPCP

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

5'-NUCLEOTIDASE

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

1hpu__assembly_3__model_1

1hpu__assembly_3__model_1 | I(q)

1hpu__assembly_3__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 (3)

5'-NUCLEOTIDASE (CLOSED FORM), COMPLEX WITH AMPCP

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

5'-NUCLEOTIDASE

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

1hpu__assembly_3__model_1

1hpu__assembly_3__model_1 | I(q)

1hpu__assembly_3__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 (3)