SAXSdb — 6yi9

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

Phosphoenolpyruvate carboxykinase, cytosolic [GTP]

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	1,2-ETHANEDIOL × 20 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PCKGC_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–622； UniProt 1–622

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	6yi9
Deposition date deposition_date	2020-04-01
Structure title title	Crystal structure of the rat cytosolic PCK1, acetylated on Lys244
Keywords keywords	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.

6yi9__assembly_1__model_1

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

Download this curve (.dat)

6yi9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6yi9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.73 Å
Rg (electron density)	24.63 Å
Total Rg	25.51 Å
Atom count	4952
Residues	619
Excluded volume	88509 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6yi9__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 (3)

Entity 1 Entity 1 polymer

Description description	Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
Molecular weight formula_weight	69540.7 kDa
EC 编号 ec_number	4.1.1.32
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	5387

MPPQLHNGLDFSAKVIQGSLDSLPQEVRKFVEGNAQLCQPEYIHICDGSEEEYGRLLAHMQEEGVIRKLKKYDNCWLALTDPRDVARIESKTVIITQEQRDTVPIPKSGQSQLGRWMSEEDFEKAFNARFPGCMKGRTMYVIPFSMGPLGSPLAKIGIELTDSPYVVASMRIMTRMGTSVLEALGDGEFIKCLHSVGCPLPLKKPLVNNWACNPELTLIAHLPDRREIISFGSGYGGNSLLGKKCFALRIASRLAKEEGWLAEHMLILGITNPEGKKKYLAAAFPSACGKTNLAMMNPTLPGWKVECVGDDIAWMKFDAQGNLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLAPGVTITSWKNKEWRPQDEEPCAHPNSRFCTPASQCPIIDPAWESPEGVPIEGIIFGGRRPAGVPLVYEALSWQHGVFVGAAMRSEATAAAEHKGKVIMHDPFAMRPFFGYNFGKYLAHWLSMAHRPAAKLPKIFHVNWFRKDKNGKFLWPGFGENSRVLEWMFGRIEGEDSAKLTPIGYVPKEDALNLKGLGDVNVEELFGISKEFWEKEVEEIDKYLEDQVNADLPYEIERELRALKQRISQM

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway Rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	20

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	435

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6yi9a1
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	d6yi9a2
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

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Unit-cell length a length_a	60.384 Å
Unit-cell length b length_b	85.225 Å
Unit-cell length c length_c	119.669 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	19.950 Å
R factor r_factor	0.1720
R_work r_work	0.1704
R_free r_free	0.2115

Crystal structure of the rat cytosolic PCK1, acetylated on Lys244

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

Phosphoenolpyruvate carboxykinase, cytosolic [GTP]

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

6yi9__assembly_1__model_1

6yi9__assembly_1__model_1 | I(q)

6yi9__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) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)

Crystal structure of the rat cytosolic PCK1, acetylated on Lys244

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

Phosphoenolpyruvate carboxykinase, cytosolic [GTP]

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

6yi9__assembly_1__model_1

6yi9__assembly_1__model_1 | I(q)

6yi9__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) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)