SAXSdb — 4c1k

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

2-DEHYDRO-3-DEOXYPHOSPHOHEPTONATE ALDOLASE

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	PHOSPHOENOLPYRUVATE × 4 CADMIUM ION × 4 CHLORIDE ION × 4 NONAETHYLENE GLYCOL × 2 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	CARBONATE ION × 4 PHOSPHOENOLPYRUVATE × 4 CADMIUM ION × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8U0A9_PYRFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–262； UniProt 1–262 Author chain B； PDBConstruct 1–262； UniProt 1–262 Author chain C； PDBConstruct 1–262； UniProt 1–262 Author chain D； PDBConstruct 1–262； UniProt 1–262 Author chain E； PDBConstruct 1–262； UniProt 1–262 Author chain F； PDBConstruct 1–262； UniProt 1–262

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	4c1k
Deposition date deposition_date	2013-08-13
Structure title title	Crystal structure of pyrococcus furiosus 3-deoxy-D-arabino- heptulosonate 7-phosphate synthase
Keywords keywords	TRANSFERASE, SHIKIMATE PATHWAY; 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.

4c1k__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4c1k__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4c1k__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	30.55 Å
Rg (electron density)	29.76 Å
Total Rg	30.38 Å
Atom count	8284
Residues	1048
Excluded volume	148750 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4c1k__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4c1k__assembly_2__model_1`	tetrameric （4）	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	2-DEHYDRO-3-DEOXYPHOSPHOHEPTONATE ALDOLASE
Molecular weight formula_weight	29260.7 kDa
EC 编号 ec_number	2.5.1.54
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	12953

MKYSKEYKEKTVVKINDVKFGEGFTIIAGPCSIESRDQIMKVAEFLAEVGIKVLRGGAFKPRTSPYSFQGYGEKALRWMREAADEYGLVTVTEVMDTRHVELVAKYSDILQIGARNSQNFELLKEVGKVENPVLLKRGMGNTIQELLYSAEYIMAQGNENVILCERGIRTFETATRFTLDISAVPVVKELSHLPIIVDPSHPAGRRSLVIPLAKAAYAIGADGIMVEVHPEPEKALSDSQQQLTFDDFLQLLKELEALGWKG

Entity 2 Entity 2 non-polymer

Description description	CARBONATE ION
Molecular weight formula_weight	60.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	PHOSPHOENOLPYRUVATE
Molecular weight formula_weight	168.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	NONAETHYLENE GLYCOL
Molecular weight formula_weight	414.5 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	416

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	4c1kA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	4c1kB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	4c1kC00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	4c1kD00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	4c1kE00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	4c1kF00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

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Unit-cell length a length_a	185.449 Å
Unit-cell length b length_b	79.670 Å
Unit-cell length c length_c	144.215 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	119.69 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

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

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	19.650 Å
R factor r_factor	0.1907
R_work r_work	0.1886
R_free r_free	0.2309

Crystal structure of pyrococcus furiosus 3-deoxy-D-arabino- heptulosonate 7-phosphate synthase

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

2-DEHYDRO-3-DEOXYPHOSPHOHEPTONATE ALDOLASE

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

4c1k__assembly_2__model_1

4c1k__assembly_2__model_1 | I(q)

4c1k__assembly_2__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

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of pyrococcus furiosus 3-deoxy-D-arabino- heptulosonate 7-phosphate synthase

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

2-DEHYDRO-3-DEOXYPHOSPHOHEPTONATE ALDOLASE

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

4c1k__assembly_2__model_1

4c1k__assembly_2__model_1 | I(q)

4c1k__assembly_2__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

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)