SAXSdb — 3h9u

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

Adenosylhomocysteinase

Trypanosoma brucei

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 8 ADENOSINE × 8 GLYCEROL × 2 TETRAETHYLENE GLYCOL × 2 water × 8	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 8	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 8 ADENOSINE × 8 GLYCEROL × 2 TETRAETHYLENE GLYCOL × 2 water × 8	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 ADENOSINE × 4 GLYCEROL × 1 TETRAETHYLENE GLYCOL × 1 water × 4	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 4	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 ADENOSINE × 4 GLYCEROL × 1 TETRAETHYLENE GLYCOL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q383X0_9TRYP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–436； UniProt 4–437 Author chain B； PDBConstruct 3–436； UniProt 4–437 Author chain C； PDBConstruct 3–436； UniProt 4–437 Author chain D； PDBConstruct 3–436； UniProt 4–437

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	3h9u
Deposition date deposition_date	2009-04-30
Structure title title	S-adenosyl homocysteine hydrolase (SAHH) from Trypanosoma brucei
Keywords keywords	;NAD co-factor complex, Structural Genomics, SGC Stockholm, Structural Genomics Consortium, SGC, Hydrolase, NAD, One-carbon metabolism ;; 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.

3h9u__assembly_1__model_1

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

Download this curve (.dat)

3h9u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3h9u__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	62.20 Å
Rg (electron density)	63.50 Å
Total Rg	63.29 Å
Atom count	27254
Residues	3458
Excluded volume	484080 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3h9u__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3h9u__assembly_2__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3h9u__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3h9u__assembly_4__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 (6)

Entity 1 Entity 1 polymer

Description description	Adenosylhomocysteinase
Molecular weight formula_weight	48380.4 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	14413

SMYKVRDISLAEWGRRELELAENEMPGLMELRREYGPSKPLKGAKIAGCLHMTMQTAVLIETLVELGAEVRWASCNIFSTQDHAAAAIAKRGIPVFAWKGETEEEYMWCMKQTLKGFSGDGYPNMLLDDGGDLTNYVLDECKELDGKIYGVSEETTTGVKNLYKRLQRGKLTIPAMNVNDSVTKSKFDNLYGCRESLVDGIKRATDVMIAGKTACVCGYGDVGKGCAAALRGFGARVVVTEVDPINALQAAMEGYQVLLVEDVVEEAHIFVTTTGNDDIITSEHFPRMRDDAIVCNIGHFDTEIQVAWLKANAKERVEVKPQVDRYTMANGRHIILLAEGRLVNLGCASGHPSFVMSNSFCNQVLAQIELWTNRDTGKYPRGAKAQVYFLPKKLDEKVAALHLGKLGAKLTKLTPKQAEYINCPVDGPFKPDHYRY

Source Source

Source organism organism	Trypanosoma brucei
NCBI taxonomy ID ncbi_taxonomy_id	5691
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	4

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE
Molecular weight formula_weight	267.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	759

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	3h9uA01
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	3h9uA02
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	3h9uB01
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	3h9uB02
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	3h9uC01
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	3h9uC02
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	3h9uD01
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	3h9uD02
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	91.350 Å
Unit-cell length b length_b	136.050 Å
Unit-cell length c length_c	191.870 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.32 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	45.550 Å
R factor r_factor	0.1981
R_work r_work	0.1965
R_free r_free	0.2306

S-adenosyl homocysteine hydrolase (SAHH) from Trypanosoma brucei

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3h9u__assembly_1__model_1

3h9u__assembly_1__model_1 | I(q)

3h9u__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

S-adenosyl homocysteine hydrolase (SAHH) from Trypanosoma brucei

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3h9u__assembly_1__model_1

3h9u__assembly_1__model_1 | I(q)

3h9u__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)