SAXSdb — 6f20

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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	Ethyl 1H-pyrrolo[2,3-b]pyridine-4-carboxylate × 1 SULFATE ION × 5 ACETATE ION × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	Ethyl 1H-pyrrolo[2,3-b]pyridine-4-carboxylate × 1 SULFATE ION × 1 ACETATE ION × 1 GLYCEROL × 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 4–159； UniProt 42–197 Author chain B； PDBConstruct 4–159； 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	6f20
Deposition date deposition_date	2017-11-23
Structure title title	Complex between MTH1 and compound 1 (a 7-azaindole-4-ester derivative)
Keywords keywords	NUDIX, NUCLEOTIDE HYDROLASE, INHIBITOR, ONCOLOGY, 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.

6f20__assembly_1__model_1

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

Download this curve (.dat)

6f20__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6f20__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.68 Å
Rg (electron density)	15.12 Å
Total Rg	16.44 Å
Atom count	1313
Residues	156
Excluded volume	23212 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6f20__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6f20__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 (6)

Entity 1 Entity 1 polymer

Description description	7,8-dihydro-8-oxoguanine triphosphatase
Molecular weight formula_weight	18253.7 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	2693

GSHMGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV

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	Ethyl 1H-pyrrolo[2,3-b]pyridine-4-carboxylate
Molecular weight formula_weight	190.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	99

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6f20a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.113 — Nudix
Superfamily Superfamily superfamily	d.113.1 — Nudix
Family Family family	d.113.1.1 — MutT-like

Domain ID domain_id	d6f20b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.113 — Nudix
Superfamily Superfamily superfamily	d.113.1 — Nudix
Family Family family	d.113.1.1 — MutT-like

CATH v4.4 (2 domains)

Domain ID domain_id	6f20A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily	10 — Nucleoside Triphosphate Pyrophosphohydrolase

Domain ID domain_id	6f20B00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily	10 — Nucleoside Triphosphate Pyrophosphohydrolase

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Unit-cell length a length_a	60.150 Å
Unit-cell length b length_b	68.220 Å
Unit-cell length c length_c	82.620 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	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	48.630 Å
R factor r_factor	0.1992
R_work r_work	0.1973
R_free r_free	0.2352

Complex between MTH1 and compound 1 (a 7-azaindole-4-ester derivative)

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

6f20__assembly_1__model_1

6f20__assembly_1__model_1 | I(q)

6f20__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

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Complex between MTH1 and compound 1 (a 7-azaindole-4-ester derivative)

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

6f20__assembly_1__model_1

6f20__assembly_1__model_1 | I(q)

6f20__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

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)