SAXSdb — 5vy2

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

U8 snoRNA-decapping enzyme

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–195 Chain B； UniProt 1–195	Mutation：A22V, F36A	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 9.5；293 K；PEG 8000, CHES	Resolution 2.30 Å R-free 0.253

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 5VY2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2XSQ Crystal structure of human Nudix motif 16 (NUDT16) in complex with IMP and magnesium Deposited 2010-09-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–195（195 aa）	Not recorded	IMP INOSINIC ACID × 2 MG MAGNESIUM ION × 4 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；PROTEIN WAS MIXED WITH 5MM MGCL2 AND 2MM IDP PRIOR SETTING-UP THE PLATES. THEN IT WAS CRYSTALLIZED FROM 20MM MGCL2, 22% W/V POLYACRYLIC ACID 5100 AND 0.1M HEPES PH 7.5.	Resolution 1.72 Å R-free 0.181
3COU Crystal structure of human Nudix motif 16 (NUDT16) Deposited 2008-03-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–195（195 aa）	Mutation：A22V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；277 K；0.1M CHES pH 9.5, 20% (w/v) PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.80 Å R-free 0.217
3COU Crystal structure of human Nudix motif 16 (NUDT16) Deposited 2008-03-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–195（195 aa）	Mutation：A22V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；277 K；0.1M CHES pH 9.5, 20% (w/v) PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.80 Å R-free 0.217
3MGM Crystal structure of human NUDT16 Deposited 2010-04-07	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–195（195 aa） Chain B 1–195（195 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；1M imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.80 Å R-free 0.201
5W6X Crystal structure of the HsNUDT16 in complex with Mg+2 and ADP-ribose Deposited 2017-06-18	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–195（195 aa） Chain B 1–195（195 aa）	Mutation：A22V Mutation：A22V	APR ADENOSINE-5-DIPHOSPHORIBOSE × 2 MG MAGNESIUM ION × 4 ACY ACETIC ACID × 2 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 9.5；293 K；PEG 8000, CHES	Resolution 2.10 Å R-free 0.238
5W6Z Crystal structure of the H24W mutant of HsNUDT16 Deposited 2017-06-18	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–195（195 aa） Chain B 1–195（195 aa）	Mutation：A22V, H24W Mutation：A22V, H24W	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 9.5；293 K；PEG 8000, CHES	Resolution 2.61 Å R-free 0.303
5W6Z Crystal structure of the H24W mutant of HsNUDT16 Deposited 2017-06-18	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain D 1–195（195 aa） Chain E 1–195（195 aa）	Mutation：A22V, H24W Mutation：A22V, H24W	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 9.5；293 K；PEG 8000, CHES	Resolution 2.61 Å R-free 0.303
5WJI Crystal structure of the F61S mutant of HsNUDT16 Deposited 2017-07-23	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–195（195 aa） Chain B 1–195（195 aa）	Mutation：A22V, F61S Mutation：A22V, F61S	CL CHLORIDE ION × 2 SO4 SULFATE ION × 1 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 9.5；293 K；PEG 8000, CHES	Resolution 2.30 Å R-free 0.277
6B09 Crystal structure of HsNUDT16 in complex with diADPR (soaked) Deposited 2017-09-14	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–195（195 aa） Chain B 1–195（195 aa）	Mutation：A22V Mutation：A22V	C7G [(2~{R},3~{S},4~{S},5~{S})-5-(6-aminopurin-9-yl)-4-[(2~{S},3~{S},4~{S},5~{S})-5-[[[[(2~{R},3~{R},4~{S},5~{S})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methyl phosphono hydrogen phosphate × 2 MG MAGNESIUM ION × 4 CL CHLORIDE ION × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 9.5；293 K；PEG 8000, CHES	Resolution 3.20 Å R-free 0.279
6CO2 Structure of an engineered protein (NUDT16TI) in complex with 53BP1 Tudor domains Deposited 2018-03-10	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–195（195 aa） Chain B 1–195（195 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M sodium citrate tribasic dehydrate, pH 5.6, 0.2 M ammonium acetate, 10% PEG 4,000	Resolution 2.49 Å R-free 0.270
6X7U Crystal Structure of the Human Nudix Hydrolase Nudt16 in complex with FAD Deposited 2020-05-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–184（184 aa） Chain C 1–184（184 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 MN MANGANESE (II) ION × 4 AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium chloride and 20% (w/v) PEG 3350	Resolution 2.70 Å R-free 0.231
6X7V Crystal Structure of the Human Nudix Hydrolase Nudt16 Deposited 2020-05-30	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–195（195 aa） Chain B 1–195（195 aa）	Not recorded	MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.2 M ammonium chloride, 20% (w/v) PEG 3350, 0.1 M MES pH 5.5	Resolution 2.30 Å R-free 0.287
6X7V Crystal Structure of the Human Nudix Hydrolase Nudt16 Deposited 2020-05-30	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–195（195 aa） Chain D 1–195（195 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.2 M ammonium chloride, 20% (w/v) PEG 3350, 0.1 M MES pH 5.5	Resolution 2.30 Å R-free 0.287

10 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NUD16_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–195； UniProt 1–195 Author chain B； PDBConstruct 1–195； UniProt 1–195

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	5vy2
Deposition date deposition_date	2017-05-24
Structure title title	Crystal structure of the F36A mutant of HsNUDT16
Keywords keywords	;nudix, nudix hydrolase, decapping enzyme, demodification of parylation, demodification of marylation, ADPribose, di-ADPribose, HYDROLASE ;; 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	22.55 Å
Radius of gyration Rg (electron density) rg_electron	21.24 Å
Forward intensity I(0) i0	26636800.00
Molecular weight molecular_weight	39216.0 kDa
Excluded volume excluded_volume	49109 Å³
Envelope volume envelope_volume	59083 Å³
Hydration-shell volume shell_volume	23373 Å³
Envelope diameter envelope_diameter	77.3 Å
Shell Rg shell_rg	28.21 Å
Envelope Rg envelope_rg	21.57 Å
Shape Rg shape_rg	21.24 Å
Total Rg total_rg	22.17 Å
Total atoms total_atoms	2766
Residues n_residues	357
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	77.7 Å
Rg (real space) rg_real	22.55 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	2.6640e+07
I(0) uncertainty (real space) i0_real_error	3.4220e+05
Rg (reciprocal space) rg_reciprocal	22.55 Å
I(0) (reciprocal space) i0_reciprocal	26640000.0000
Solution quality estimate total_estimate	0.8626
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.9 Å
Skewness Skewness skewness	0.416
Kurtosis Kurtosis kurtosis	-0.123
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6117000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.746; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.980

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	U8 snoRNA-decapping enzyme
Molecular weight formula_weight	21254.3 kDa
EC 编号 ec_number	3.6.1.62,3.6.1.64
Mutation mutation	A22V, F36A
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	2964

MAGARRLELGEALALGSGWRHVCHALLYAPDPGMLAGRIPLRYAILMQMRFDGRLGFPGGFVDTQDRSLEDGLNRELREELGEAAAAFRVERTDYRSSHVGSGPRVVAHFYAKRLTLEELLAVEAGATRAKDHGLEVLGLVRVPLYTLRDGVGGLPTFLENSFIGSAREQLLEALQDLGLLQSGSISGLKIPAHH

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	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	176

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5vy2A00
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	5vy2B00
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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8. Citations (1)

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Unit-cell length a length_a	57.202 Å
Unit-cell length b length_b	49.589 Å
Unit-cell length c length_c	64.284 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.59 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1919
R_work r_work	0.1889
R_free r_free	0.2533

fit	/app/data/saxs_computation/vy/5vy2/5vy2.fit
pddf	/app/data/pr_computation/vy/5vy2/5vy2.pr.out
profile	/app/data/saxs_computation/vy/5vy2/5vy2.dat

Crystal structure of the F36A mutant of HsNUDT16

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

U8 snoRNA-decapping enzyme

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