SAXSdb — 8qhq

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

;2'-deoxynucleoside 5'-phosphate N-hydrolase 1 ;

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	5-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE × 2 1,2-ETHANEDIOL × 4 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	5-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE × 2 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	5-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE × 2 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DNPH1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–147； UniProt 19–162 Author chain B； PDBConstruct 4–147； UniProt 19–162 Author chain C； PDBConstruct 4–147； UniProt 19–162 Author chain D； PDBConstruct 4–147； UniProt 19–162 Author chain E； PDBConstruct 4–147； UniProt 19–162 Author chain F； PDBConstruct 4–147； UniProt 19–162

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	8qhq
Deposition date deposition_date	2023-09-09
Last revision last_revision	2023-11-08
Structure title title	Crystal structure of human DNPH1 bound to hmdUMP
Keywords keywords	DNPH1 N-glycosidase hmdUMP, 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.

8qhq__assembly_3__model_1

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

Download this curve (.dat)

8qhq__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8qhq__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	19.25 Å
Rg (electron density)	18.23 Å
Total Rg	19.04 Å
Atom count	4260
Residues	264
Excluded volume	37885 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8qhq__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8qhq__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`8qhq__assembly_3__model_1`	dimeric （2）	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	;2'-deoxynucleoside 5'-phosphate N-hydrolase 1 ;
Molecular weight formula_weight	16337.4 kDa
EC 编号 ec_number	3.2.2.-
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	14365

GSMGRPALYFCGSIRGGREDRTLYERIVSRLRRFGTVLTEHVAAAELGARGEEAAGGDRLIHEQDLEWLQQADVVVAEVTQPSLGVGYQLGRAVAFNKRILCLFRPQSGRVLSAMIRGAADGSRFQVWDYEEGEVEALLDRYFEADP

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	5-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE
Molecular weight formula_weight	338.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	nat
Copy count entity_count	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	498

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Unit-cell length a length_a	56.648 Å
Unit-cell length b length_b	67.126 Å
Unit-cell length c length_c	120.117 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.63 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	1.780 Å
Low-resolution limit resolution_low	55.850 Å
R factor r_factor	0.2066
R_work r_work	0.2056
R_free r_free	0.2244

Crystal structure of human DNPH1 bound to hmdUMP

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

;2'-deoxynucleoside 5'-phosphate N-hydrolase 1 ;

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

8qhq__assembly_3__model_1

8qhq__assembly_3__model_1 | I(q)

8qhq__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

7. Citations (1)

Crystal structure of human DNPH1 bound to hmdUMP

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

;2'-deoxynucleoside 5'-phosphate N-hydrolase 1 ;

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

8qhq__assembly_3__model_1

8qhq__assembly_3__model_1 | I(q)

8qhq__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

7. Citations (1)