1k0u

Inhibition of S-adenosylhomocysteine Hydrolase by "acyclic sugar" Adenosine Analogue D-eritadenine

Method: X-RAY DIFFRACTION

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

S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 D-ERITADENINE × 4 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 D-ERITADENINE × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

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 Author chain E； PDBConstruct 1–431； UniProt 1–431 Author chain F； PDBConstruct 1–431； UniProt 1–431 Author chain G； PDBConstruct 1–431； UniProt 1–431 Author chain H； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1k0u
Deposition date deposition_date	2001-09-20
Structure title title	Inhibition of S-adenosylhomocysteine Hydrolase by "acyclic sugar" Adenosine Analogue D-eritadenine
Keywords keywords	S-adenosylhomocysteine, hydrolase, D-eritadenine, inhibitor; 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.

1k0u__assembly_1__model_1

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

Download this curve (.dat)

1k0u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1k0u__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.61 Å
Rg (electron density)	34.17 Å
Total Rg	34.60 Å
Atom count	13524
Residues	1720
Excluded volume	241420 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1k0u__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1k0u__assembly_2__model_1`	tetrameric （4）	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 (4)

Entity 1 Entity 1 polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE 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	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	27522

ADKLPYKVADIGLAAWGRKALDIAENEMPGLMRMREMYSASKPLKGARIAGCLHMTVETAVLIETLVALGAEVRWSSCNIFSTQDHAAAAIAKAGIPVFAWKGETDEEYLWCIEQTLHFKDGPLNMILDDGGDLTNLIHTKHPQLLSGIRGISEETTTGVHNLYKMMANGILKVPAINVNDSVTKSKFDNLYGCRESLIDGIKRATDVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPINALQAAMEGYEVTTMDEACKEGNIFVTTTGCVDIILGRHFEQMKDDAIVCNIGHFDVEIDVKWLNENAVEKVNIKPQVDRYLLKNGHRIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVMAQIELWTHPDKYPVGVHFLPKKLDEAVAEAHLGKLNVKLTKLTEKQAQYLGMPINGPFKPDHYRY

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism 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	8

Entity 3 Entity 3 non-polymer

Description description	D-ERITADENINE
Molecular weight formula_weight	253.2 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	474

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d1k0ua1
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	d1k0ua2
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	d1k0ub1
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	d1k0ub2
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	d1k0uc1
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	d1k0uc2
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	d1k0ud1
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	d1k0ud2
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	d1k0ue1
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	d1k0ue2
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	d1k0uf1
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	d1k0uf2
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	d1k0ug1
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	d1k0ug2
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	d1k0uh1
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	d1k0uh2
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 (16 domains)

Domain ID domain_id	1k0uA01
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	1k0uA02
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	1k0uB01
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	1k0uB02
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	1k0uC01
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	1k0uC02
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	1k0uD01
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	1k0uD02
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	1k0uE01
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	1k0uE02
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	1k0uF01
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	1k0uF02
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	1k0uG01
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	1k0uG02
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	1k0uH01
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	1k0uH02
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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Unit-cell length a length_a	89.870 Å
Unit-cell length b length_b	177.370 Å
Unit-cell length c length_c	112.160 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.60 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1830
R_work r_work	0.1830
R_free r_free	0.2650

Inhibition of S-adenosylhomocysteine Hydrolase by "acyclic sugar" Adenosine Analogue D-eritadenine

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

S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE

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

1k0u__assembly_1__model_1

1k0u__assembly_1__model_1 | I(q)

1k0u__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (1)

Inhibition of S-adenosylhomocysteine Hydrolase by "acyclic sugar" Adenosine Analogue D-eritadenine

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

S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE

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

1k0u__assembly_1__model_1

1k0u__assembly_1__model_1 | I(q)

1k0u__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (1)