SAXSdb — 4yvf

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

Adenosylhomocysteinase

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–432 Chain B； UniProt 1–432	Not recorded	NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 4 XFA 2-{[5-chloro-2-(4-chlorophenoxy)phenyl](2-{[2-(methylamino)ethyl]amino}-2-oxoethyl)amino}-N-(1,3-dihydro-2H-isoindol-2-yl)-N-methylacetamide × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；HEPES, PEG 4000, 2-propanol, ethyl acetate	Resolution 2.70 Å R-free 0.239

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 4YVF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A7A STRUCTURE OF HUMAN PLACENTAL S-ADENOSYLHOMOCYSTEINE HYDROLASE: DETERMINATION OF A 30 SELENIUM ATOM SUBSTRUCTURE FROM DATA AT A SINGLE WAVELENGTH Deposited 1998-03-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–432（431 aa） Chain B 2–432（431 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 ADC (1'R,2'S)-9-(2-HYDROXY-3'-KETO-CYCLOPENTEN-1-YL)ADENINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.6	Resolution 2.80 Å R-free 0.247
1LI4 Human S-adenosylhomocysteine hydrolase complexed with neplanocin Deposited 2002-04-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–432（432 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 NOC 3-(6-AMINO-PURIN-9-YL)-5-HYDROXYMETHYL-CYCLOPENTANE-1,2-DIOL × 4 IPA ISOPROPYL ALCOHOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；273 K；PEG4K, IOSPROPANOL, AMMONIUM ACETATE, CITRATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 2.01 Å R-free 0.236
3NJ4 Fluoro-neplanocin A in Human S-Adenosylhomocysteine Hydrolase Deposited 2010-06-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–432（432 aa） Chain B 1–432（432 aa） Chain C 1–432（432 aa） Chain D 1–432（432 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 AFX (4S,5S)-4-(6-amino-9H-purin-9-yl)-3-fluoro-5-hydroxy-2-(hydroxymethyl)cyclopent-2-en-1-one × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M HEPES pH 8.0, 22% PEG400, 100mM Lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.261
4PFJ The structure of bi-acetylated SAHH Deposited 2014-04-29	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–432（432 aa） Chain B 1–432（432 aa）	Mutation：e396c Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：e396c Non-standard monomer：Yes (specific site not provided by mmCIF)	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 ADN ADENOSINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；PEG 3350, sodium formate, bis-tris	Resolution 2.30 Å R-free 0.245
4PGF The structure of mono-acetylated SAHH Deposited 2014-05-01	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–432（432 aa） Chain B 1–432（432 aa）	Mutation：e396c Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：e396c Non-standard monomer：Yes (specific site not provided by mmCIF)	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 ADN ADENOSINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；PEG 3350, sodium formate, bis-tris	Resolution 2.59 Å R-free 0.248
5W49 The crystal structure of human S-adenosylhomocysteine hydrolase (AHCY) bound to oxadiazole inhibitor Deposited 2017-06-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 4–432（429 aa） Chain B 4–432（429 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 EDO 1,2-ETHANEDIOL × 28 9W1 (4-amino-1,2,5-oxadiazol-3-yl)[(3R)-3-{4-[(3-methoxyphenyl)amino]-6-methylpyridin-2-yl}pyrrolidin-1-yl]methanone × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；8-12% PEG8000, 0.12 M ethylene glycol, 0.1 M Tris(base):Bicine, pH 8.5	Resolution 2.40 Å R-free 0.226
5W4B The crystal structure of human S-adenosylhomocysteine hydrolase (AHCY) bound to benzothiazole inhibitor Deposited 2017-06-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 4–432（429 aa） Chain B 4–432（429 aa） Chain E 4–432（429 aa） Chain F 4–432（429 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 9W4 4-[(2,5-dioxo-2,5-dihydro-1H-imidazol-1-yl)methyl]-N-[2-(morpholin-4-yl)-1,3-benzothiazol-6-yl]benzamide × 4 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；8-12% PEG8000, 0.12 M ethylene glycol, 0.1 M Tris(base):Bicine, pH 8.5	Resolution 2.65 Å R-free 0.240
5W4B The crystal structure of human S-adenosylhomocysteine hydrolase (AHCY) bound to benzothiazole inhibitor Deposited 2017-06-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain C 4–432（429 aa） Chain D 4–432（429 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 9W4 4-[(2,5-dioxo-2,5-dihydro-1H-imidazol-1-yl)methyl]-N-[2-(morpholin-4-yl)-1,3-benzothiazol-6-yl]benzamide × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；8-12% PEG8000, 0.12 M ethylene glycol, 0.1 M Tris(base):Bicine, pH 8.5	Resolution 2.65 Å R-free 0.240
9QYI Crystal structure of human S-adenosyl-L-homocysteine hydrolase complex with adenosine Deposited 2025-04-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–432（431 aa） Chain B 2–432（431 aa） Chain D 2–432（431 aa） Chain E 2–432（431 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 ADN ADENOSINE × 4 K POTASSIUM ION × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；Morpheus D4	Resolution 1.59 Å R-free 0.214
9QYI Crystal structure of human S-adenosyl-L-homocysteine hydrolase complex with adenosine Deposited 2025-04-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain C 2–432（431 aa） Chain F 2–432（431 aa） Chain G 2–432（431 aa） Chain H 2–432（431 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 ADN ADENOSINE × 4 K POTASSIUM ION × 5 SO4 SULFATE ION × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；Morpheus D4	Resolution 1.59 Å R-free 0.214
9QYJ Crystal structure of human S-adenosyl-L-homocysteine hydrolase in complex with adenosine and cadmium ions. Deposited 2025-04-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–432（431 aa） Chain B 2–432（431 aa） Chain D 2–432（431 aa） Chain E 2–432（431 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 ADN ADENOSINE × 4 CD CADMIUM ION × 24 K POTASSIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；Morpheus D4	Resolution 1.93 Å R-free 0.244
9QYJ Crystal structure of human S-adenosyl-L-homocysteine hydrolase in complex with adenosine and cadmium ions. Deposited 2025-04-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain C 2–432（431 aa） Chain F 2–432（431 aa） Chain G 2–432（431 aa） Chain H 2–432（431 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 ADN ADENOSINE × 4 CD CADMIUM ION × 21 K POTASSIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；Morpheus D4	Resolution 1.93 Å R-free 0.244

9 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SAHH_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–432； UniProt 1–432 Author chain B； PDBConstruct 1–432； UniProt 1–432

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	4yvf
Deposition date deposition_date	2015-03-20
Structure title title	Structure of S-adenosyl-L-homocysteine hydrolase
Keywords keywords	SAHH, 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	29.90 Å
Radius of gyration Rg (electron density) rg_electron	29.44 Å
Forward intensity I(0) i0	149232000.00
Molecular weight molecular_weight	97197.0 kDa
Excluded volume excluded_volume	121680 Å³
Envelope volume envelope_volume	141450 Å³
Hydration-shell volume shell_volume	39548 Å³
Envelope diameter envelope_diameter	97.7 Å
Shell Rg shell_rg	37.09 Å
Envelope Rg envelope_rg	29.48 Å
Shape Rg shape_rg	29.46 Å
Total Rg total_rg	30.02 Å
Total atoms total_atoms	6808
Residues n_residues	858
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	92.7 Å
Rg (real space) rg_real	29.82 Å
Rg uncertainty (real space) rg_real_error	0.58 Å
I(0) (real space) i0_real	1.4920e+08
I(0) uncertainty (real space) i0_real_error	2.2250e+06
Rg (reciprocal space) rg_reciprocal	29.85 Å
I(0) (reciprocal space) i0_reciprocal	149200000.0000
Solution quality estimate total_estimate	0.9049
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.0 Å
Skewness Skewness skewness	0.231
Kurtosis Kurtosis kurtosis	-0.503
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	64250000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.951; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.907

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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	Adenosylhomocysteinase
Molecular weight formula_weight	47773.0 kDa
EC 编号 ec_number	3.3.1.1
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	7052

MSDKLPYKVADIGLAAWGRKALDIAENEMPGLMRMRERYSASKPLKGARIAGCLHMTVETAVLIETLVTLGAEVQWSSCNIFSTQDHAAAAIAKAGIPVYAWKGETDEEYLWCIEQTLYFKDGPLNMILDDGGDLTNLIHTKYPQLLPGIRGISEETTTGVHNLYKMMANGILKVPAINVNDSVTKSKFDNLYGCRESLIDGIKRATDVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPINALQAAMEGYEVTTMDEACQEGNIFVTTTGCIDIILGRHFEQMKDDAIVCNIGHFDVEIDVKWLNENAVEKVNIKPQVDRYRLKNGRRIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVMAQIELWTHPDKYPVGVHFLPKKLDEAVAEAHLGKLNVKLTKLTEKQAQYLGMSCDGPFKPDHYRY

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	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
Molecular weight formula_weight	665.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	;2-{[5-chloro-2-(4-chlorophenoxy)phenyl](2-{[2-(methylamino)ethyl]amino}-2-oxoethyl)amino}-N-(1,3-dihydro-2H-isoindol-2-yl)-N-methylacetamide ;
Molecular weight formula_weight	556.5 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	244

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4yvfa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.12 — Formate/glycerate dehydrogenase catalytic domain-like
Family Family family	c.23.12.3 — S-adenosylhomocystein hydrolase

Domain ID domain_id	d4yvfa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.4 — Formate/glycerate dehydrogenases, NAD-domain

Domain ID domain_id	d4yvfb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.12 — Formate/glycerate dehydrogenase catalytic domain-like
Family Family family	c.23.12.3 — S-adenosylhomocystein hydrolase

Domain ID domain_id	d4yvfb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.4 — Formate/glycerate dehydrogenases, NAD-domain

CATH v4.4 (4 domains)

Domain ID domain_id	4yvfA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1480 — Adenosylhomocysteinase-like

Domain ID domain_id	4yvfA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	4yvfB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1480 — Adenosylhomocysteinase-like

Domain ID domain_id	4yvfB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

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8. Citations (1)

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Unit-cell length a length_a	91.528 Å
Unit-cell length b length_b	134.150 Å
Unit-cell length c length_c	185.164 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	47.810 Å
R factor r_factor	0.1990
R_work r_work	0.1990
R_free r_free	0.2390

fit	/app/data/saxs_computation/yv/4yvf/4yvf.fit
pddf	/app/data/pr_computation/yv/4yvf/4yvf.pr.out
profile	/app/data/saxs_computation/yv/4yvf/4yvf.dat

Structure of S-adenosyl-L-homocysteine hydrolase

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

Adenosylhomocysteinase

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