7aks

Human ADP-ribosylserine hydrolase ARH3 mutant E41A in complex with H2B-S7-mar peptide

Method: X-RAY DIFFRACTION

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

ADP-ribose glycohydrolase ARH3

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	modified peptide × 1 MAGNESIUM ION × 2 1,2-ETHANEDIOL × 3 ACETATE ION × 6 ;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ; × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	modified peptide × 1 MAGNESIUM ION × 3 1,2-ETHANEDIOL × 6 ACETATE ION × 8 ;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ; × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	modified peptide × 1 MAGNESIUM ION × 2 1,2-ETHANEDIOL × 7 ACETATE ION × 7 ;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ; × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	modified peptide × 1 MAGNESIUM ION × 2 1,2-ETHANEDIOL × 3 ACETATE ION × 7 ;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ; × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ADPRS_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain AAA； PDBConstruct 5–349； UniProt 19–363 Author chain CCC； PDBConstruct 5–349； UniProt 19–363 Author chain EEE； PDBConstruct 5–349； UniProt 19–363 Author chain GGG； PDBConstruct 5–349； UniProt 19–363

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	7aks
Deposition date deposition_date	2020-10-02
Structure title title	Human ADP-ribosylserine hydrolase ARH3 mutant E41A in complex with H2B-S7-mar peptide
Keywords keywords	ADP-RIBOSYLATION, ADP-RIBOSE, ADPRHL2, ADP-RIBOSYLHYDROLASE LIKE 2, SER-ADPR, SERINE-ADPR, ADP-RIBOSYL-L-SERINE, 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.

7aks__assembly_1__model_1

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

Download this curve (.dat)

7aks__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7aks__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.60 Å
Rg (electron density)	18.50 Å
Total Rg	19.40 Å
Atom count	2623
Residues	334
Excluded volume	46246 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7aks__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7aks__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`7aks__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`7aks__assembly_4__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 (7)

Entity 1 Entity 1 polymer

Description description	ADP-ribose glycohydrolase ARH3
Molecular weight formula_weight	37796.3 kDa
EC 编号 ec_number	3.5.1.-,3.2.1.143,3.2.2.-
Mutation mutation	E41A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AAA,CCC,EEE,GGG
Atom count atom_count	11678

GPGSSLSRFRGCLAGALLGDCVGSFYAAHDTVDLTSVLRHVQSLEPDPGTPGSERTEALYYTDDTAMARALVQSLLAKEAFDEVDMAHRFAQEYKKDPDRGYGAGVVTVFKKLLNPKCRDVFEPARAQFNGKGSYGNGGAMRVAGISLAYSSVQDVQKFARLSAQLTHASSLGYNGAILQALAVHLALQGESSSEHFLKQLLGHMEDLEGDAQSVLDARELGMEERPYSSRLKKIGELLDQASVTREEVVSELGNGIAAFESVPTAIYCFLRCMEPDPEIPSAFNSLQRTLIYSISLGGDTDTIATMAGAIAGAYYGMDQVPESWQQSCEGYEETDILAQSLHRVFQKS

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 polymer

Description description	modified peptide
Molecular weight formula_weight	1096.3 kDa
EC 编号 ec_number	3.5.1.-,3.2.1.143,3.2.2.-
Mutation mutation	E41A
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	BaB,DaD,FaF,HaH

PAKSAPAPKKG

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	9

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	19

Entity 5 Entity 5 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	28

Entity 6 Entity 6 non-polymer

Description description	;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ;
Molecular weight formula_weight	559.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	758

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Unit-cell length a length_a	123.360 Å
Unit-cell length b length_b	158.638 Å
Unit-cell length c length_c	74.920 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	16

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.860 Å
Low-resolution limit resolution_low	97.572 Å
R factor r_factor	—
R_work r_work	0.1685
R_free r_free	0.1946

Human ADP-ribosylserine hydrolase ARH3 mutant E41A in complex with H2B-S7-mar peptide

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

ADP-ribose glycohydrolase ARH3

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

7aks__assembly_1__model_1

7aks__assembly_1__model_1 | I(q)

7aks__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

Human ADP-ribosylserine hydrolase ARH3 mutant E41A in complex with H2B-S7-mar peptide

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

ADP-ribose glycohydrolase ARH3

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

7aks__assembly_1__model_1

7aks__assembly_1__model_1 | I(q)

7aks__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)