SAXSdb — 2z1k

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

(Neo)pullulanase

Thermus thermophilus

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	Cycloheptakis-(1-4)-(alpha-D-glucopyranose) × 1 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 water × 1	Consistent with protein count
2	Other combination	Monomer	Protein 1 其他Polymer 2	Cycloheptakis-(1-4)-(alpha-D-glucopyranose) × 1 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 water × 1	Consistent with protein count
3	Other combination	Monomer	Protein 1 其他Polymer 2	Cycloheptakis-(1-4)-(alpha-D-glucopyranose) × 1 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 water × 1	Consistent with protein count
4	Other combination	Monomer	Protein 1 其他Polymer 2	Cycloheptakis-(1-4)-(alpha-D-glucopyranose) × 1 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 PHOSPHATE ION × 1 water × 1	Consistent with protein count
5	Other combination	Homooligomer	Protein 2 其他Polymer 4	Cycloheptakis-(1-4)-(alpha-D-glucopyranose) × 2 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 2 water × 2	Consistent with protein count
6	Other combination	Homooligomer	Protein 2 其他Polymer 4	Cycloheptakis-(1-4)-(alpha-D-glucopyranose) × 2 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 2 PHOSPHATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5SI17_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–475； UniProt 1–475 Author chain B； PDBConstruct 1–475； UniProt 1–475 Author chain C； PDBConstruct 1–475； UniProt 1–475 Author chain D； PDBConstruct 1–475； UniProt 1–475

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	2z1k
Deposition date deposition_date	2007-05-08
Structure title title	Crystal Structure of Ttha1563 from Thermus thermophilus HB8
Keywords keywords	;HYDROLASE, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI ;; 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.

2z1k__assembly_1__model_1

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

Download this curve (.dat)

2z1k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2z1k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.10 Å
Rg (electron density)	23.14 Å
Total Rg	23.89 Å
Atom count	3913
Residues	467
Excluded volume	69511 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2z1k__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2z1k__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2z1k__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2z1k__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2z1k__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2z1k__assembly_6__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 (5)

Entity 1 Entity 1 polymer

Description description	(Neo)pullulanase
Molecular weight formula_weight	54200.4 kDa
EC 编号 ec_number	3.2.1.41
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	16422

MAWYEGAFFYQIFPDRFFRAGPPGRPAPAGPFEPWEAPPTLRGFKGGTLWGVAEKLPYLLDLGVEAIYLNPVFASTANHRYHTVDYFQVDPILGGNEALRHLLEVAHAHGVRVILDGVFNHTGRGFFAFQHLMENGEQSPYRDWYHVKGFPLKAYTAHPNYEAWWGNPELPKLKVETPAVREYLLAVAEHWIRFGVDGWRLDVPNEIPDPTFWREFRQRVKGANPEAYIVGEIWEEADFWLQGDMFDAVMNYPLARAVLGFVGGEALDRDLAAQTGLGRIEPLQALAFSHRLEDLFGRYRPEVVRAQMNLLTSHDTPRLLSLMRGSVERARLALALLFLLPGNPTVYYGEEVGMAGGKDPENRGGMVWEEARWQKDLRETVKRLARLRKEHPALRTAPYLRIYAQDGHLAFARGPYLAVVNASPHPFRQDFPLHGVFPRGGRAVDLLSGEVCTPQGGRLCGPVLPPFSLALWREA

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	Cycloheptakis-(1-4)-(alpha-D-glucopyranose)
Molecular weight formula_weight	1153.0 kDa
Source method src_method	man
Copy count entity_count	4

Entity 3 Entity 3 branched

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

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 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	781

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	2z1kA01
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	2z1kA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

Domain ID domain_id	2z1kB01
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	2z1kB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

Domain ID domain_id	2z1kC01
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	2z1kC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

Domain ID domain_id	2z1kD01
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	2z1kD02
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	67.144 Å
Unit-cell length b length_b	95.897 Å
Unit-cell length c length_c	140.598 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	46.660 Å
R factor r_factor	0.1850
R_work r_work	0.1850
R_free r_free	0.2360

Crystal Structure of Ttha1563 from Thermus thermophilus HB8

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

(Neo)pullulanase

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

2z1k__assembly_1__model_1

2z1k__assembly_1__model_1 | I(q)

2z1k__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 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal Structure of Ttha1563 from Thermus thermophilus HB8

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

(Neo)pullulanase

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

2z1k__assembly_1__model_1

2z1k__assembly_1__model_1 | I(q)

2z1k__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 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)