SAXSdb — 3bcd

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

Alpha amylase, catalytic region

Halothermothrix orenii

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 3	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 Cyclohexakis-(1-4)-(alpha-D-glucopyranose) × 1 CALCIUM ION × 7 SODIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q2ADF2_9FIRM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–599； UniProt 25–623

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	3bcd
Deposition date deposition_date	2007-11-12
Structure title title	Alpha-amylase B in complex with maltotetraose and alpha-cyclodextrin
Keywords keywords	alpha-amylase, maltotetraose, alpha-cyclodextrin, thermostable, halophilic, N domain, raw starch binding, 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.

3bcd__assembly_1__model_1

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

Download this curve (.dat)

3bcd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bcd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.34 Å
Rg (electron density)	27.60 Å
Total Rg	28.22 Å
Atom count	4911
Residues	585
Excluded volume	86403 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bcd__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 (7)

Entity 1 Entity 1 polymer

Description description	Alpha amylase, catalytic region
Molecular weight formula_weight	68580.9 kDa
EC 编号 ec_number	3.2.1.1
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	5170

GCSNISEDVNNPNRSLFLIESEPSTGASVSKNLTEIILIFSNDINKVSQLALTDLITDSDIQGIDYNIEGNKVIINNFSLEPTCNYRLSYEVIDIYDNHLQGYIEFLVNQSNYPQIPDQEVNHTILQAFYWEMNTGEYATEHPEEANLWNLLAERAPELAEAGFTAVWLPPANKGMAGIHDVGYGTYDLWDLGEFDQKGTVRTKYGTKGELENAIDALHNNDIKVYFDAVLNHRMGADYAETVLLDENSRDKPGQYIKAWTGFNFPGRNGEYSNFTWNGQCFDGTDWDDYSKESGKYLFDEKSWDWTYNWDEDYLMGADVDYENEAVQNDVIDWGQWIINNIDFDGFRLDAVKHIDYRFIDKWMSAVQNSSNRDVFFVGEAWVEDVDDLKGFLDTVGNPDLRVFDFPLRSFFVDMLNGAYMADLRNAGLVNSPGYENRAVTFVDNHDTDRDEGSYTVSIYSRKYQAYAYILTRAEGVPTVYWKDYYIWEMKEGLDKLLTARRYYAYGPGYEVDNNDADIYSYVRSGFPDVAGDGLVLMISDGTSGNVAGKWINSRQPDTEFYDLTGHIKEHVTTDSEGYGNFKVIKSEDKGWSIWVPVE

Source Source

Source organism organism	Halothermothrix orenii
NCBI taxonomy ID ncbi_taxonomy_id	373903
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 branched

Description description	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose
Molecular weight formula_weight	666.6 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)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
Molecular weight formula_weight	666.6 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 branched

Description description	Cyclohexakis-(1-4)-(alpha-D-glucopyranose)
Molecular weight formula_weight	990.9 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 6 Entity 6 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	259

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3bcdA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1220 —

Domain ID domain_id	3bcdA02
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	3bcdA03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	3bcdA04
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	228.700 Å
Unit-cell length b length_b	78.050 Å
Unit-cell length c length_c	50.640 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.90 °
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	2.200 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1968
R_work r_work	0.1960
R_free r_free	0.2401

Alpha-amylase B in complex with maltotetraose and alpha-cyclodextrin

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

Alpha amylase, catalytic region

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

3bcd__assembly_1__model_1

3bcd__assembly_1__model_1 | I(q)

3bcd__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Alpha-amylase B in complex with maltotetraose and alpha-cyclodextrin

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

Alpha amylase, catalytic region

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

3bcd__assembly_1__model_1

3bcd__assembly_1__model_1 | I(q)

3bcd__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)