SAXSdb — 2d0f

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

alpha-amylase I

Thermoactinomyces vulgaris

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 2	;alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose ; × 1 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 CALCIUM ION × 3 (4S)-2-METHYL-2,4-PENTANEDIOL × 4 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NEPU1_THEVU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–637； UniProt 30–666

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	2d0f
Deposition date deposition_date	2005-08-02
Structure title title	Crystal Structure of Thermoactinomyces vulgaris R-47 Alpha-Amylase 1 (TVAI) Mutant D356N complexed with P2, a pullulan model oligosaccharide
Keywords keywords	ALPHA-AMYLASE, Hydrolase; 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.

2d0f__assembly_1__model_1

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

Download this curve (.dat)

2d0f__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2d0f__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.80 Å
Rg (electron density)	25.83 Å
Total Rg	26.62 Å
Atom count	5163
Residues	637
Excluded volume	90426 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2d0f__assembly_1__model_1`	monomeric （1）	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	alpha-amylase I
Molecular weight formula_weight	71109.3 kDa
EC 编号 ec_number	3.2.1.1
Mutation mutation	D356N
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5615

AANDNNVEWNGLFHDQGPLFDNAPEPTSTQSVTLKLRTFKGDITSANIKYWDTADNAFHWVPMVWDSNDPTGTFDYWKGTIPASPSIKYYRFQINDGTSTAWYNGNGPSSTEPNADDFYIIPNFKTPDWLKNGVMYQIFPDRFYNGDSSNDVQTGSYTYNGTPTEKKAWGSSVYADPGYDNSLVFFGGDLAGIDQKLGYIKKTLGANILYLNPIFKAPTNHKYDTQDYMAVDPAFGDNSTLQTLINDIHSTANGPKGYLILDGVFNHTGDSHPWFDKYNNFSSQGAYESQSSPWYNYYTFYTWPDSYASFLGFNSLPKLNYGNSGSAVRGVIYNNSNSVAKTYLNPPYSVDGWRLNAAQYVDANGNNGSDVTNHQIWSEFRNAVKGVNSNAAIIGEYWGNANPWTAQGNQWDAATNFDGFTQPVSEWITGKDYQNNSASISTTQFDSWLRGTRANYPTNVQQSMMNFLSNHDITRFATRSGGDLWKTYLALIFQMTYVGTPTIYYGDEYGMQGGADPDNRRSFDWSQATPSNSAVALTQKLITIRNQYPALRTGSFMTLITDDTNKIYSYGRFDNVNRIAVVLNNDSVSHTVNVPVWQLSMPNGSTVTDKITGHSYTVQNGMVTVAVDGHYGAVLAQ

Source Source

Source organism organism	Thermoactinomyces vulgaris
NCBI taxonomy ID ncbi_taxonomy_id	2026
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	;alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose ;
Molecular weight formula_weight	828.7 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 branched

Description description	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose
Molecular weight formula_weight	504.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	452

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2d0fa1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.0 — automated matches

Domain ID domain_id	d2d0fa2
Class class	b — All beta proteins
Fold Fold fold	b.71 — Glycosyl hydrolase domain
Superfamily Superfamily superfamily	b.71.1 — Glycosyl hydrolase domain
Family Family family	b.71.1.0 — automated matches

Domain ID domain_id	d2d0fa3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.1 — Amylase, catalytic domain

CATH v4.4 (3 domains)

Domain ID domain_id	2d0fA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2d0fA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

Domain ID domain_id	2d0fA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

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Unit-cell length a length_a	121.532 Å
Unit-cell length b length_b	50.429 Å
Unit-cell length c length_c	107.834 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.30 °
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	2.080 Å
Low-resolution limit resolution_low	46.000 Å
R factor r_factor	0.1570
R_work r_work	0.1540
R_free r_free	0.1870

Crystal Structure of Thermoactinomyces vulgaris R-47 Alpha-Amylase 1 (TVAI) Mutant D356N complexed with P2, a pullulan model oligosaccharide

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

alpha-amylase I

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

2d0f__assembly_1__model_1

2d0f__assembly_1__model_1 | I(q)

2d0f__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 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal Structure of Thermoactinomyces vulgaris R-47 Alpha-Amylase 1 (TVAI) Mutant D356N complexed with P2, a pullulan model oligosaccharide

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

alpha-amylase I

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

2d0f__assembly_1__model_1

2d0f__assembly_1__model_1 | I(q)

2d0f__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 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)