SAXSdb — 4iqy

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

O-acetyl-ADP-ribose deacetylase MACROD2

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 7–243	Fragment：macrodomain (UNP residues 7-243)	AR6 [(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 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；18% PEG3350, 0.1M HEPES, 0.1M MgFormate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.55 Å R-free 0.187
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 7–243	Fragment：macrodomain (UNP residues 7-243)	AR6 [(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 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；18% PEG3350, 0.1M HEPES, 0.1M MgFormate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.55 Å R-free 0.187

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 4IQY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6Y4Y The crystal structure of human MACROD2 in space group P41212 Deposited 2020-02-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 7–243（237 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；293 K；0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350	Resolution 1.75 Å R-free 0.227
6Y4Y The crystal structure of human MACROD2 in space group P41212 Deposited 2020-02-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 7–243（237 aa）	Not recorded	TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；293 K；0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350	Resolution 1.75 Å R-free 0.227
6Y4Y The crystal structure of human MACROD2 in space group P41212 Deposited 2020-02-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 7–243（237 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；293 K；0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350	Resolution 1.75 Å R-free 0.227
6Y4Y The crystal structure of human MACROD2 in space group P41212 Deposited 2020-02-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain D 7–243（237 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；293 K；0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350	Resolution 1.75 Å R-free 0.227
6Y4Z The crystal structure of human MACROD2 in space group P43212 Deposited 2020-02-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 7–243（237 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；293 K；0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350	Resolution 1.90 Å R-free 0.228
6Y4Z The crystal structure of human MACROD2 in space group P43212 Deposited 2020-02-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 7–243（237 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；293 K；0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350	Resolution 1.90 Å R-free 0.228
6Y4Z The crystal structure of human MACROD2 in space group P43212 Deposited 2020-02-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 7–243（237 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；293 K；0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350	Resolution 1.90 Å R-free 0.228
6Y4Z The crystal structure of human MACROD2 in space group P43212 Deposited 2020-02-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain D 7–243（237 aa）	Not recorded	TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；293 K；0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350	Resolution 1.90 Å R-free 0.228
6Y73 The crystal structure of human MACROD2 in space group P43 Deposited 2020-02-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 7–243（237 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；293 K；0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350	Resolution 1.70 Å R-free 0.203
6Y73 The crystal structure of human MACROD2 in space group P43 Deposited 2020-02-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 7–243（237 aa）	Not recorded	GOL GLYCEROL × 1 TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；293 K；0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350	Resolution 1.70 Å R-free 0.203
6Y73 The crystal structure of human MACROD2 in space group P43 Deposited 2020-02-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 7–243（237 aa）	Not recorded	GOL GLYCEROL × 2 TLA L(+)-TARTARIC ACID × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；293 K；0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350	Resolution 1.70 Å R-free 0.203
6Y73 The crystal structure of human MACROD2 in space group P43 Deposited 2020-02-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 7–243（237 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；293 K；0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350	Resolution 1.70 Å R-free 0.203
6Y73 The crystal structure of human MACROD2 in space group P43 Deposited 2020-02-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 7–243（237 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；293 K；0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350	Resolution 1.70 Å R-free 0.203
6Y73 The crystal structure of human MACROD2 in space group P43 Deposited 2020-02-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 7–243（237 aa）	Not recorded	TLA L(+)-TARTARIC ACID × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；293 K；0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350	Resolution 1.70 Å R-free 0.203
6Y73 The crystal structure of human MACROD2 in space group P43 Deposited 2020-02-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 7–243（237 aa）	Not recorded	TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；293 K；0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350	Resolution 1.70 Å R-free 0.203
6Y73 The crystal structure of human MACROD2 in space group P43 Deposited 2020-02-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 7–243（237 aa）	Not recorded	TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；293 K；0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350	Resolution 1.70 Å R-free 0.203

3 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MACD2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–240； UniProt 7–243 Author chain B； PDBConstruct 4–240； UniProt 7–243

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	4iqy
Deposition date deposition_date	2013-01-14
Structure title title	Crystal structure of the human protein-proximal ADP-ribosyl-hydrolase MacroD2
Keywords keywords	macrodomain, hydrolase, ADP-ribose binding, ADP-ribosylation, nuclear/cytoplasmic; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	25.80 Å
Radius of gyration Rg (electron density) rg_electron	24.80 Å
Forward intensity I(0) i0	43209900.00
Molecular weight molecular_weight	50372.0 kDa
Excluded volume excluded_volume	62918 Å³
Envelope volume envelope_volume	77241 Å³
Hydration-shell volume shell_volume	26475 Å³
Envelope diameter envelope_diameter	87.7 Å
Shell Rg shell_rg	31.28 Å
Envelope Rg envelope_rg	24.59 Å
Shape Rg shape_rg	24.79 Å
Total Rg total_rg	25.59 Å
Total atoms total_atoms	3531
Residues n_residues	440
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	86.8 Å
Rg (real space) rg_real	25.80 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	4.3210e+07
I(0) uncertainty (real space) i0_real_error	6.0130e+05
Rg (reciprocal space) rg_reciprocal	25.80 Å
I(0) (reciprocal space) i0_reciprocal	43210000.0000
Solution quality estimate total_estimate	0.8078
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.6 Å
Skewness Skewness skewness	0.301
Kurtosis Kurtosis kurtosis	-0.567
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7954000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.843; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	O-acetyl-ADP-ribose deacetylase MACROD2
Molecular weight formula_weight	27070.2 kDa
EC 编号 ec_number	3.5.1.-
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	4079

GHMKKKVWREEKERLLKMTLEERRKEYLRDYIPLNSILSWKEEMKGKGQNDEENTQETSQVKKSLTEKVSLYRGDITLLEVDAIVNAANASLLGGGGVDGCIHRAAGPCLLAECRNLNGCDTGHAKITCGYDLPAKYVIHTVGPIARGHINGSHKEDLANCYKSSLKLVKENNIRSVAFPCISTGIYGFPNEPAAVIALNTIKEWLAKNHHEVDRIIFCVFLEVDFKIYKKKMNEFFSVD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 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	2

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	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	531

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4iqyA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	4iqyB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

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8. Citations (1)

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Unit-cell length a length_a	40.713 Å
Unit-cell length b length_b	49.883 Å
Unit-cell length c length_c	66.972 Å
Unit-cell angle α angle_alpha	69.82 °
Unit-cell angle β angle_beta	72.35 °
Unit-cell angle γ angle_gamma	86.08 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	46.783 Å
R factor r_factor	0.1597
R_work r_work	0.1583
R_free r_free	0.1870

fit	/app/data/saxs_computation/iq/4iqy/4iqy.fit
pddf	/app/data/pr_computation/iq/4iqy/4iqy.pr.out
profile	/app/data/saxs_computation/iq/4iqy/4iqy.dat

Crystal structure of the human protein-proximal ADP-ribosyl-hydrolase MacroD2

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

O-acetyl-ADP-ribose deacetylase MACROD2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction