SAXSdb — 1i79

▼

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

S-ADENOSYLMETHIONINE DECARBOXYLASE BETA CHAIN

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	5'-DEOXY-5'-[(3-HYDRAZINOPROPYL)METHYLAMINO]ADENOSINE × 2 1,4-DIAMINOBUTANE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DCAM_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain B； PDBConstruct 1–67； UniProt 1–67 Author chain A； PDBConstruct 1–267； UniProt 68–334

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1i79
Deposition date deposition_date	2001-03-08
Structure title title	HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE WITH COVALENTLY BOUND PYRUVOYL GROUP AND COVALENTLY BOUND 5'-DEOXY-5'-[(3-HYDRAZINOPROPYL)METHYLAMINO]ADENOSINE
Keywords keywords	Spermidine biosynthesis, Lyase, Decarboxylase, Pyruvate, S-ADENOSYLMETHIONINE, SANDWICH, ALLOSTERIC ENZYME, PYRUVOYL; LYASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1i79__assembly_1__model_1

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

Download this curve (.dat)

1i79__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1i79__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.04 Å
Rg (electron density)	27.13 Å
Total Rg	27.98 Å
Atom count	5128
Residues	624
Excluded volume	91504 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1i79__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	S-ADENOSYLMETHIONINE DECARBOXYLASE BETA CHAIN
Molecular weight formula_weight	7694.6 kDa
EC 编号 ec_number	4.1.1.50
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	2724

MEAAHFFEGTEKLLEVWFSRQQPDANQGSGDLRTIPRSEWDILLKDVQCSIISVTKTDKQEAYVLSE

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	S-ADENOSYLMETHIONINE DECARBOXYLASE ALPHA CHAIN
Molecular weight formula_weight	30672.0 kDa
EC 编号 ec_number	4.1.1.50
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

XSMFVSKRRFILKTCGTTLLLKALVPLLKLARDYSGFDSIQSFFYSRKNFMKPSHQGYPHRNFQEEIEFLNAIFPNGAGYCMGRMNSDCWYLYTLDFPESRVISQPDQTLEILMSELDPAVMDQFYMKDGVTAKDVTRESGIRDLIPGSVIDATMFNPCGYSMNGMKSDGTYWTIHITPEPEFSYVSFETNLSQTSYDDLIRKVVEVFKPGKFVTTLFVNQSSKCRTVLASPQKIEGFKRLDCQSAMFNDYNFVFTSFAKKQQQQQS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	5'-DEOXY-5'-[(3-HYDRAZINOPROPYL)METHYLAMINO]ADENOSINE
Molecular weight formula_weight	352.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,4-DIAMINOBUTANE
Molecular weight formula_weight	88.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	160

▼

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1i79.1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.156 — S-adenosylmethionine decarboxylase
Superfamily Superfamily superfamily	d.156.1 — S-adenosylmethionine decarboxylase
Family Family family	d.156.1.1 — S-adenosylmethionine decarboxylase

CATH v4.4 (2 domains)

Domain ID domain_id	1i79A00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	90 — S-adenosylmethionine decarboxylase
Homologous superfamily homologous superfamily	10 — S-adenosylmethionine decarboxylase

Domain ID domain_id	1i79B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	50 — S-adenosylmethionine decarboxylase

▶

Unit-cell length a length_a	100.282 Å
Unit-cell length b length_b	50.751 Å
Unit-cell length c length_c	68.624 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.27 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.010 Å
Low-resolution limit resolution_low	25.380 Å
R factor r_factor	—
R_work r_work	0.2120
R_free r_free	0.2560

HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE WITH COVALENTLY BOUND PYRUVOYL GROUP AND COVALENTLY BOUND 5'-DEOXY-5'-[(3-HYDRAZINOPROPYL)METHYLAMINO]ADENOSINE

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

S-ADENOSYLMETHIONINE DECARBOXYLASE BETA CHAIN

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

1i79__assembly_1__model_1

1i79__assembly_1__model_1 | I(q)

1i79__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (2)

HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE WITH COVALENTLY BOUND PYRUVOYL GROUP AND COVALENTLY BOUND 5'-DEOXY-5'-[(3-HYDRAZINOPROPYL)METHYLAMINO]ADENOSINE

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

S-ADENOSYLMETHIONINE DECARBOXYLASE BETA CHAIN

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

1i79__assembly_1__model_1

1i79__assembly_1__model_1 | I(q)

1i79__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (2)