SAXSdb — 7a5y

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

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	FE (III) ION × 4 MAGNESIUM ION × 12 2'-deoxyguanosine-5'-O-(1-thiotriphosphate) × 12 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	FE (III) ION × 4 MAGNESIUM ION × 12 2'-deoxyguanosine-5'-O-(1-thiotriphosphate) × 12 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SAMH1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–520； UniProt 109–626 Author chain B； PDBConstruct 3–520； UniProt 109–626 Author chain C； PDBConstruct 3–520； UniProt 109–626 Author chain D； PDBConstruct 3–520； UniProt 109–626 Author chain E； PDBConstruct 3–520； UniProt 109–626 Author chain F； PDBConstruct 3–520； UniProt 109–626 Author chain G； PDBConstruct 3–520； UniProt 109–626 Author chain H； PDBConstruct 3–520； UniProt 109–626

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	7a5y
Deposition date deposition_date	2020-08-24
Structure title title	Crystal structure of tetrameric human H215A-SAMHD1 (residues 109-626) with Rp-dGTP-alphaS (T8T) and Mg
Keywords keywords	triphosphohydrolase, metallo-enzyme, binuclear, HD, 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.

7a5y__assembly_1__model_1

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

Download this curve (.dat)

7a5y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7a5y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.35 Å
Rg (electron density)	34.80 Å
Total Rg	35.38 Å
Atom count	15044
Residues	1820
Excluded volume	266400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7a5y__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7a5y__assembly_2__model_1`	tetrameric （4）	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	Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Molecular weight formula_weight	60141.7 kDa
EC 编号 ec_number	3.1.5.-
Mutation mutation	H215A
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	30465

GSQIHVDTMKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSAMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDICFIKEQIVGPLESPVEDSLWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKREDYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMDYGMQEKNPIDHVSFYCKTAPNRAIRITKNQVSQLLPEKFAEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQDGDVIAPLITPQKKEWNDSTSVQNPTRLREASKSRVQLFKDDPM

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	24

Entity 4 Entity 4 non-polymer

Description description	2'-deoxyguanosine-5'-O-(1-thiotriphosphate)
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	24

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	343

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Unit-cell length a length_a	80.193 Å
Unit-cell length b length_b	181.263 Å
Unit-cell length c length_c	286.331 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	32

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.290 Å
Low-resolution limit resolution_low	153.150 Å
R factor r_factor	0.2117
R_work r_work	0.2101
R_free r_free	0.2403

Crystal structure of tetrameric human H215A-SAMHD1 (residues 109-626) with Rp-dGTP-alphaS (T8T) and Mg

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

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

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

7a5y__assembly_1__model_1

7a5y__assembly_1__model_1 | I(q)

7a5y__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)

Crystal structure of tetrameric human H215A-SAMHD1 (residues 109-626) with Rp-dGTP-alphaS (T8T) and Mg

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

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

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

7a5y__assembly_1__model_1

7a5y__assembly_1__model_1 | I(q)

7a5y__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)