SAXSdb — 1ut8

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

EXODEOXYRIBONUCLEASE

BACTERIOPHAGE T5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EXO5_BPT5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–291； UniProt 1–290 Author chain B； PDBConstruct 2–291； UniProt 1–290

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	1ut8
Deposition date deposition_date	2003-12-04
Structure title title	Divalent metal ions (zinc) bound to T5 5'-exonuclease
Keywords keywords	EXONUCLEASE, HYDROLASE, NUCLEASE; 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.

1ut8__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1ut8__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ut8__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.63 Å
Rg (electron density)	19.68 Å
Total Rg	20.56 Å
Atom count	2205
Residues	272
Excluded volume	39257 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ut8__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1ut8__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	EXODEOXYRIBONUCLEASE
Molecular weight formula_weight	33491.9 kDa
EC 编号 ec_number	3.1.11.3
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	4624

MSKSWGKFIEEEEAEMASRRNLMIVDGTNLGFRFKHNNSKKPFASSYVSTIQSLAKSYSARTTIVLGDKGKSVFRLEHLPEYKGNRDEKYAQRTEEEKALDEQFFEYLKDAFELCKTTFPTFTIRGVEADDMAAYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSRFSFTTRREYHLRDMYEHHNVDDVEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLPGKQKYIQNLNASEELLFRNLILVDLPTYCVDAIAAVGQDVLDKFTKDILEIAEQ

Source Source

Source organism organism	BACTERIOPHAGE T5
NCBI taxonomy ID ncbi_taxonomy_id	10726
Host organism host_organism	ESCHERICHIA COLI

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	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	223

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1ut8a1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.7 — 5' to 3' exonuclease, C-terminal subdomain
Family Family family	a.60.7.1 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	d1ut8a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.120 — PIN domain-like
Superfamily Superfamily superfamily	c.120.1 — PIN domain-like
Family Family family	c.120.1.2 — 5' to 3' exonuclease catalytic domain

Domain ID domain_id	d1ut8b1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.7 — 5' to 3' exonuclease, C-terminal subdomain
Family Family family	a.60.7.1 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	d1ut8b2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.120 — PIN domain-like
Superfamily Superfamily superfamily	c.120.1 — PIN domain-like
Family Family family	c.120.1.2 — 5' to 3' exonuclease catalytic domain

CATH v4.4 (4 domains)

Domain ID domain_id	1ut8A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	1ut8A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1010 — 5'-nuclease

Domain ID domain_id	1ut8B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	1ut8B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1010 — 5'-nuclease

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Unit-cell length a length_a	77.940 Å
Unit-cell length b length_b	77.940 Å
Unit-cell length c length_c	134.690 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	8

Space group space_group	P 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	—
R_work r_work	0.2350
R_free r_free	0.3130

Divalent metal ions (zinc) bound to T5 5'-exonuclease

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

EXODEOXYRIBONUCLEASE

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

1ut8__assembly_2__model_1

1ut8__assembly_2__model_1 | I(q)

1ut8__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Divalent metal ions (zinc) bound to T5 5'-exonuclease

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

EXODEOXYRIBONUCLEASE

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

1ut8__assembly_2__model_1

1ut8__assembly_2__model_1 | I(q)

1ut8__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)