SAXSdb — 9mbi

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

7,8-dihydro-8-oxoguanine triphosphatase

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	MANGANESE (II) ION × 3 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 3 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	8ODP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–156； UniProt 42–197 Author chain B； PDBConstruct 1–156； UniProt 42–197

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	9mbi
Deposition date deposition_date	2025-03-17
Last revision last_revision	2025-07-30
Structure title title	8-Oxo-dGTP hydrolysis in human MTH1(G2K mutant) crystal using Mn2+: the ES/EP-3M complex
Keywords keywords	Oxidized purine nucleoside triphosphate hydrolase, 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.

9mbi__assembly_1__model_1

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

Download this curve (.dat)

9mbi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9mbi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.91 Å
Rg (electron density)	14.74 Å
Total Rg	15.90 Å
Atom count	2550
Residues	156
Excluded volume	23186 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9mbi__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9mbi__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 (5)

Entity 1 Entity 1 polymer

Description description	7,8-dihydro-8-oxoguanine triphosphatase
Molecular weight formula_weight	18043.6 kDa
EC 编号 ec_number	3.6.1.55,3.6.1.56
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	6153

MKASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
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	6

Entity 3 Entity 3 non-polymer

Description description	8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
Molecular weight formula_weight	363.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	411

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Unit-cell length a length_a	46.497 Å
Unit-cell length b length_b	47.637 Å
Unit-cell length c length_c	123.839 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	1.090 Å
Low-resolution limit resolution_low	32.130 Å
R factor r_factor	0.1411
R_work r_work	0.1399
R_free r_free	0.1644

8-Oxo-dGTP hydrolysis in human MTH1(G2K mutant) crystal using Mn2+: the ES/EP-3M complex

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

7,8-dihydro-8-oxoguanine triphosphatase

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

9mbi__assembly_1__model_1

9mbi__assembly_1__model_1 | I(q)

9mbi__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

7. Citations (1)

8-Oxo-dGTP hydrolysis in human MTH1(G2K mutant) crystal using Mn2+: the ES/EP-3M complex

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

7,8-dihydro-8-oxoguanine triphosphatase

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

9mbi__assembly_1__model_1

9mbi__assembly_1__model_1 | I(q)

9mbi__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

7. Citations (1)