1ky4

S-Adenosylhomocysteine hydrolase refined with noncrystallographic restraints

Method: X-RAY DIFFRACTION D_max: 111.8 Å Quality: GOOD

▼

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

S-adenosylhomocysteine hydrolase

Rattus norvegicus

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 1–431 Chain B； UniProt 1–431 Chain C； UniProt 1–431 Chain D； UniProt 1–431	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；297 K；PEG 6000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.80 Å R-free 0.278

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 1KY4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B3R RAT LIVER S-ADENOSYLHOMOCYSTEIN HYDROLASE Deposited 1998-12-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–431（431 aa） Fragment：CATALYTIC DOMAIN (1 - 181 & 352 - 402) Chain B 1–431（431 aa） Fragment：CATALYTIC DOMAIN (1 - 181 & 352 - 402) Chain C 1–431（431 aa） Fragment：CATALYTIC DOMAIN (1 - 181 & 352 - 402) Chain D 1–431（431 aa） Fragment：CATALYTIC DOMAIN (1 - 181 & 352 - 402)	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.8；50 MM TRIS/HCL (PH 6.8), 6 MM MGCL2, 5% MPD, 15% PEG-6K	Resolution 2.80 Å R-free 0.269
1D4F CRYSTAL STRUCTURE OF RECOMBINANT RAT-LIVER D244E MUTANT S-ADENOSYLHOMOCYSTEINE HYDROLASE Deposited 2000-06-22	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 1–431（431 aa） Chain B 1–431（431 aa） Chain C 1–431（431 aa） Chain D 1–431（431 aa）	Mutation：D244E Mutation：D244E Mutation：D244E Mutation：D244E	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 ADN ADENOSINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；295 K；22% PEG 4000, 50 mM Tris/HCl, 2% glycerol, 10% isopropanol, and 1 mM DTT. Protein concentration is 10 mg/mL., pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.80 Å R-free 0.248
1K0U Inhibition of S-adenosylhomocysteine Hydrolase by "acyclic sugar" Adenosine Analogue D-eritadenine Deposited 2001-09-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–431（431 aa） Chain B 1–431（431 aa） Chain C 1–431（431 aa） Chain D 1–431（431 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 DEA D-ERITADENINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；295 K；PEG 4000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.00 Å R-free 0.265
1K0U Inhibition of S-adenosylhomocysteine Hydrolase by "acyclic sugar" Adenosine Analogue D-eritadenine Deposited 2001-09-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 1–431（431 aa） Chain F 1–431（431 aa） Chain G 1–431（431 aa） Chain H 1–431（431 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 DEA D-ERITADENINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；295 K；PEG 4000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.00 Å R-free 0.265
1KY5 D244E mutant S-Adenosylhomocysteine hydrolase refined with noncrystallographic restraints Deposited 2002-02-03	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–431（431 aa） Chain B 1–431（431 aa） Chain C 1–431（431 aa） Chain D 1–431（431 aa）	Mutation：D244E Mutation：D244E Mutation：D244E Mutation：D244E	NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 4 ADY 3'-OXO-ADENOSINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；297 K；PEG 6000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.80 Å R-free 0.293
1XWF K185N mutated S-adenosylhomocysteine hydrolase Deposited 2004-11-01	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 1–431（431 aa） Chain B 1–431（431 aa） Chain C 1–431（431 aa） Chain D 1–431（431 aa）	Mutation：K185N Mutation：K185N Mutation：K185N Mutation：K185N	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 ADN ADENOSINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；PEG4000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.286
2H5L S-Adenosylhomocysteine hydrolase containing NAD and 3-deaza-D-eritadenine Deposited 2006-05-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–431（431 aa） Chain B 1–431（431 aa） Chain C 1–431（431 aa） Chain D 1–431（431 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 3DD (2R,3R)-4-(4-AMINO-1H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-2,3-DIHYDROXYBUTANOIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；295 K；15% PGE-8000, 50 mM MES, 2% glycerol, pH 6.5, VAPOR DIFFUSION, temperature 295K	Resolution 2.80 Å R-free 0.283
2H5L S-Adenosylhomocysteine hydrolase containing NAD and 3-deaza-D-eritadenine Deposited 2006-05-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 1–431（431 aa） Chain F 1–431（431 aa） Chain G 1–431（431 aa） Chain H 1–431（431 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 3DD (2R,3R)-4-(4-AMINO-1H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-2,3-DIHYDROXYBUTANOIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；295 K；15% PGE-8000, 50 mM MES, 2% glycerol, pH 6.5, VAPOR DIFFUSION, temperature 295K	Resolution 2.80 Å R-free 0.283

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SAHH_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–431； UniProt 1–431 Author chain B； PDBConstruct 1–431； UniProt 1–431 Author chain C； PDBConstruct 1–431； UniProt 1–431 Author chain D； PDBConstruct 1–431； UniProt 1–431

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1ky4
Deposition date deposition_date	2002-02-03
Structure title title	S-Adenosylhomocysteine hydrolase refined with noncrystallographic restraints
Keywords keywords	hydrolase, S-adenosylhomocysteine; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	35.79 Å
Radius of gyration Rg (electron density) rg_electron	35.40 Å
Forward intensity I(0) i0	549132000.00
Molecular weight molecular_weight	191000.0 kDa
Excluded volume excluded_volume	239220 Å³
Envelope volume envelope_volume	282250 Å³
Hydration-shell volume shell_volume	63803 Å³
Envelope diameter envelope_diameter	117.6 Å
Shell Rg shell_rg	43.70 Å
Envelope Rg envelope_rg	35.31 Å
Shape Rg shape_rg	35.44 Å
Total Rg total_rg	35.75 Å
Total atoms total_atoms	13384
Residues n_residues	1712
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

▼

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

Maximum dimension Dmax dmax	111.8 Å
Rg (real space) rg_real	35.62 Å
Rg uncertainty (real space) rg_real_error	0.85 Å
I(0) (real space) i0_real	5.4910e+08
I(0) uncertainty (real space) i0_real_error	9.8300e+06
Rg (reciprocal space) rg_reciprocal	35.73 Å
I(0) (reciprocal space) i0_reciprocal	549200000.0000
Solution quality estimate total_estimate	0.8908
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	45.8 Å
Skewness Skewness skewness	0.209
Kurtosis Kurtosis kurtosis	-0.383
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	135600000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.874

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	S-adenosylhomocysteine hydrolase
Molecular weight formula_weight	47465.7 kDa
EC 编号 ec_number	3.3.1.1
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	13650

ADKLPYKVADIGLAAWGRKALDIAENEMPGLMRMREMYSASKPLKGARIAGCLHMTVETAVLIETLVALGAEVRWSSCNIFSTQDHAAAAIAKAGIPVFAWKGETDEEYLWCIEQTLHFKDGPLNMILDDGGDLTNLIHTKHPQLLSGIRGISEETTTGVHNLYKMMANGILKVPAINVNDSVTKSKFDNLYGCRESLIDGIKRATDVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPINALQAAMEGYEVTTMDEACKEGNIFVTTTGCVDIILGRHFEQMKDDAIVCNIGHFDVEIDVKWLNENAVEKVNIKPQVDRYLLKNGHRIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVMAQIELWTHPDKYPVGVHFLPKKLDEAVAEAHLGKLNVKLTKLTEKQAQYLGMPINGPFKPDHYRY

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	266

▼

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1ky4a1
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	d1ky4a2
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	d1ky4b1
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	d1ky4b2
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	d1ky4c1
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	d1ky4c2
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	d1ky4d1
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	d1ky4d2
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

CATH v4.4 (8 domains)

Domain ID domain_id	1ky4A01
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	1ky4A02
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	1ky4B01
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	1ky4B02
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	1ky4C01
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	1ky4C02
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	1ky4D01
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	1ky4D02
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

▶

8. Citations (1)

▶

Unit-cell length a length_a	94.760 Å
Unit-cell length b length_b	134.480 Å
Unit-cell length c length_c	102.260 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.35 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2290
R_work r_work	0.2280
R_free r_free	0.2780

fit	/app/data/saxs_computation/ky/1ky4/1ky4.fit
pddf	/app/data/pr_computation/ky/1ky4/1ky4.pr.out
profile	/app/data/saxs_computation/ky/1ky4/1ky4.dat