SAXSdb — 1k1y

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

4-ALPHA-GLUCANOTRANSFERASE

Thermococcus litoralis

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 1	;4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose ; × 1 CALCIUM ION × 1 water × 1	Consistent with protein count
2	Other combination	Monomer	Protein 1 其他Polymer 1	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 CALCIUM ION × 2 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 1	Consistent with protein count
3	Other combination	Homooligomer	Protein 2 其他Polymer 2	;4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose ; × 1 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 CALCIUM ION × 3 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MALQ_THELI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–659； UniProt 1–659 Author chain B； PDBConstruct 1–659； UniProt 1–659

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	1k1y
Deposition date deposition_date	2001-09-26
Structure title title	Crystal structure of thermococcus litoralis 4-alpha-glucanotransferase complexed with acarbose
Keywords keywords	4-ALPHA-GLUCANOTRANSFERASE COMPLEXED WITH ACARBOSE, TRANSFERASE; TRANSFERASE
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.

1k1y__assembly_1__model_1

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

Download this curve (.dat)

1k1y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1k1y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.14 Å
Rg (electron density)	27.51 Å
Total Rg	28.34 Å
Atom count	5393
Residues	636
Excluded volume	96725 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1k1y__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1k1y__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1k1y__assembly_3__model_1`	dimeric （2）	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	4-ALPHA-GLUCANOTRANSFERASE
Molecular weight formula_weight	77989.1 kDa
EC 编号 ec_number	2.4.1.25
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	11345

MERINFIFGIHNHQPLGNFGWVFEEAYNRSYRPFMEILEEFPEMKVNVHFSGPLLEWIEENKPDYLDLLRSLIKRGQLEIVVAGFYEPVLAAIPKEDRLVQIEMLKDYARKLGYDAKGVWLTERVWQPELVKSLREAGIEYVVVDDYHFMSAGLSKEELFWPYYTEDGGEVITVFPIDEKLRYLIPFRPVKKTIEYLESLTSDDPSKVAVFHDDGEKFGVWPGTYEWVYEKGWLREFFDAITSNEKINLMTYSEYLSKFTPRGLVYLPIASYFEMSEWSLPAKQAKLFVEFVEQLKEEGKFEKYRVFVRGGIWKNFFFKYPESNFMHKRMLMVSKAVRDNPEARKYILKAQCNDAYWHGVFGGIYLPHLRRTVWENIIKAQRYLKPENKILDVDFDGRAEIMVENDGFIATIKPHYGGSIFELSSKRKAVNYNDVLPRRWEHYHEVPEATKPEKESEEGIASIHELGKQIPEEIRRELAYDWQLRAILQDHFIKPEETLDNYRLVKYHELGDFVNQPYEYEMIENGVKLWREGGVYAEEKIPARVEKKIELTEDGFIAKYRVLLEKPYKALFGVEINLAVHSVMEKPEEFEAKEFEVNDPYGIGKVRIELDKAAKVWKFPIKTLSQSEAGWDFIQQGVSYTMLFPIEKELEFTVRFREL

Source Source

Source organism organism	Thermococcus litoralis
NCBI taxonomy ID ncbi_taxonomy_id	2265
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 branched

Description description	;4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose ;
Molecular weight formula_weight	645.6 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
Molecular weight formula_weight	342.3 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	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 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	572

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1k1ya1
Class class	a — All alpha proteins
Fold Fold fold	a.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamily	a.8.3 — Families 57/38 glycoside transferase middle domain
Family Family family	a.8.3.2 — 4-alpha-glucanotransferase, domain 2

Domain ID domain_id	d1k1ya2
Class class	b — All beta proteins
Fold Fold fold	b.30 — Supersandwich
Superfamily Superfamily superfamily	b.30.5 — Galactose mutarotase-like
Family Family family	b.30.5.8 — 4-alpha-glucanotransferase, C-terminal domain

Domain ID domain_id	d1k1ya3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.6 — 7-stranded beta/alpha barrel
Superfamily Superfamily superfamily	c.6.2 — Glycoside hydrolase/deacetylase
Family Family family	c.6.2.2 — 4-alpha-glucanotransferase, N-terminal domain

Domain ID domain_id	d1k1yb1
Class class	a — All alpha proteins
Fold Fold fold	a.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamily	a.8.3 — Families 57/38 glycoside transferase middle domain
Family Family family	a.8.3.2 — 4-alpha-glucanotransferase, domain 2

Domain ID domain_id	d1k1yb2
Class class	b — All beta proteins
Fold Fold fold	b.30 — Supersandwich
Superfamily Superfamily superfamily	b.30.5 — Galactose mutarotase-like
Family Family family	b.30.5.8 — 4-alpha-glucanotransferase, C-terminal domain

Domain ID domain_id	d1k1yb3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.6 — 7-stranded beta/alpha barrel
Superfamily Superfamily superfamily	c.6.2 — Glycoside hydrolase/deacetylase
Family Family family	c.6.2.2 — 4-alpha-glucanotransferase, N-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id	1k1yA01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	110 — 7-stranded beta/alpha barrel
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1k1yA02
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1k1yB01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	110 — 7-stranded beta/alpha barrel
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1k1yB02
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	137.610 Å
Unit-cell length b length_b	160.968 Å
Unit-cell length c length_c	70.202 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	39.850 Å
R factor r_factor	0.1980
R_work r_work	0.1980
R_free r_free	0.2560

Crystal structure of thermococcus litoralis 4-alpha-glucanotransferase complexed with acarbose

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

4-ALPHA-GLUCANOTRANSFERASE

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

1k1y__assembly_1__model_1

1k1y__assembly_1__model_1 | I(q)

1k1y__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) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of thermococcus litoralis 4-alpha-glucanotransferase complexed with acarbose

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

4-ALPHA-GLUCANOTRANSFERASE

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

1k1y__assembly_1__model_1

1k1y__assembly_1__model_1 | I(q)

1k1y__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) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)