SAXSdb — 6at4

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

Phosphoenolpyruvate carboxykinase (ATP)

Escherichia coli K-12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	THIOSULFATE × 3 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	THIOSULFATE × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PCKA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–540； UniProt 1–540 Author chain B； PDBConstruct 1–540； UniProt 1–540

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	6at4
Deposition date deposition_date	2017-08-27
Structure title title	E. coli phosphoenolpyruvate carboxykinase bound to thiosulfate
Keywords keywords	Nonnative ligand, LYASE; LYASE
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.

6at4__assembly_1__model_1

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

Download this curve (.dat)

6at4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6at4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.82 Å
Rg (electron density)	22.77 Å
Total Rg	23.61 Å
Atom count	8074
Residues	535
Excluded volume	73474 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6at4__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6at4__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	Phosphoenolpyruvate carboxykinase (ATP)
Molecular weight formula_weight	60538.1 kDa
EC 编号 ec_number	4.1.1.49
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	17105

MRVNNGLTPQELEAYGISDVHDIVYNPSYDLLYQEELDPSLTGYERGVLTNLGAVAVDTGIFTGRSPKDKYIVRDDTTRDTFWWADKGKGKNDNKPLSPETWQHLKGLVTRQLSGKRLFVVDAFCGANPDTRLSVRFITEVAWQAHFVKNMFIRPSDEELAGFKPDFIVMNGAKCTNPQWKEQGLNSENFVAFNLTERMQLIGGTWYGGEMKKGMFSMMNYLLPLKGIASMHCSANVGEKGDVAVFFGLSGTGKTTLSTDPKRRLIGDDEHGWDDDGVFNFEGGCYAKTIKLSKEAEPEIYNAIRRDALLENVTVREDGTIDFDDGSKTENTRVSYPIYHIDNIVKPVSKAGHATKVIFLTADAFGVLPPVSRLTADQTQYHFLSGFTAKLAGTERGITEPTPTFSACFGAAFLSLHPTQYAEVLVKRMQAAGAQAYLVNTGWNGTGKRISIKDTRAIIDAILNGSLDNAETFTLPMFNLAIPTELPGVDTKILDPRNTYASPEQWQEKAETLAKLFIDNFDKYTDTPAGAALVAAGPKLHHHHHH

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	THIOSULFATE
Molecular weight formula_weight	112.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	926

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6at4a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.109 — PEP carboxykinase N-terminal domain
Superfamily Superfamily superfamily	c.109.1 — PEP carboxykinase N-terminal domain
Family Family family	c.109.1.1 — PEP carboxykinase N-terminal domain

Domain ID domain_id	d6at4a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.91 — PEP carboxykinase-like
Superfamily Superfamily superfamily	c.91.1 — PEP carboxykinase-like
Family Family family	c.91.1.1 — PEP carboxykinase C-terminal domain

Domain ID domain_id	d6at4b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.109 — PEP carboxykinase N-terminal domain
Superfamily Superfamily superfamily	c.109.1 — PEP carboxykinase N-terminal domain
Family Family family	c.109.1.1 — PEP carboxykinase N-terminal domain

Domain ID domain_id	d6at4b2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.91 — PEP carboxykinase-like
Superfamily Superfamily superfamily	c.91.1 — PEP carboxykinase-like
Family Family family	c.91.1.1 — PEP carboxykinase C-terminal domain

CATH v4.4 (6 domains)

Domain ID domain_id	6at4A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	449 — Phosphoenolpyruvate Carboxykinase; domain 1
Homologous superfamily homologous superfamily	10 — Phosphoenolpyruvate Carboxykinase, domain 1

Domain ID domain_id	6at4A02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	8 — Phosphoenolpyruvate Carboxykinase; domain 2
Homologous superfamily homologous superfamily	10 — Phosphoenolpyruvate Carboxykinase, domain 2

Domain ID domain_id	6at4A03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	228 — Phosphoenolpyruvate Carboxykinase; domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	6at4B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	449 — Phosphoenolpyruvate Carboxykinase; domain 1
Homologous superfamily homologous superfamily	10 — Phosphoenolpyruvate Carboxykinase, domain 1

Domain ID domain_id	6at4B02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	8 — Phosphoenolpyruvate Carboxykinase; domain 2
Homologous superfamily homologous superfamily	10 — Phosphoenolpyruvate Carboxykinase, domain 2

Domain ID domain_id	6at4B03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	228 — Phosphoenolpyruvate Carboxykinase; domain 3
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	94.720 Å
Unit-cell length b length_b	103.614 Å
Unit-cell length c length_c	119.156 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.332 Å
Low-resolution limit resolution_low	78.188 Å
R factor r_factor	0.1352
R_work r_work	0.1350
R_free r_free	0.1514

E. coli phosphoenolpyruvate carboxykinase bound to thiosulfate

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

Phosphoenolpyruvate carboxykinase (ATP)

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

6at4__assembly_1__model_1

6at4__assembly_1__model_1 | I(q)

6at4__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)

E. coli phosphoenolpyruvate carboxykinase bound to thiosulfate

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

Phosphoenolpyruvate carboxykinase (ATP)

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

6at4__assembly_1__model_1

6at4__assembly_1__model_1 | I(q)

6at4__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)