3dtb

The structure of rat cytosolic PEPCK in complex with phosphoglycolate and GDP

Method: X-RAY DIFFRACTION

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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	2-PHOSPHOGLYCOLIC ACID × 1 MANGANESE (II) ION × 2 SODIUM ION × 1 BICARBONATE ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 PENTAETHYLENE GLYCOL × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	2-PHOSPHOGLYCOLIC ACID × 1 MANGANESE (II) ION × 2 SODIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	2-PHOSPHOGLYCOLIC ACID × 2 MANGANESE (II) ION × 4 SODIUM ION × 2 BICARBONATE ION × 1 GUANOSINE-5'-DIPHOSPHATE × 2 PENTAETHYLENE GLYCOL × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PPCKC_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–624； UniProt 1–622 Author chain B； PDBConstruct 3–624； 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	3dtb
Deposition date deposition_date	2008-07-14
Structure title title	The structure of rat cytosolic PEPCK in complex with phosphoglycolate and GDP
Keywords keywords	kinase, gluconeogenesis, lyase, Decarboxylase, GTP-binding, Nucleotide-binding; 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.

3dtb__assembly_1__model_1

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

Download this curve (.dat)

3dtb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dtb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.39 Å
Rg (electron density)	24.41 Å
Total Rg	25.23 Å
Atom count	4948
Residues	620
Excluded volume	88170 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dtb__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3dtb__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3dtb__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 (9)

Entity 1 Entity 1 polymer

Description description	Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
Molecular weight formula_weight	69643.8 kDa
EC 编号 ec_number	4.1.1.32
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	11713

GSMPPQLHNGLDFSAKVIQGSLDSLPQEVRKFVEGNAQLCQPEYIHICDGSEEEYGRLLAHMQEEGVIRKLKKYDNCWLALTDPRDVARIESKTVIITQEQRDTVPIPKSGQSQLGRWMSEEDFEKAFNARFPGCMKGRTMYVIPFSMGPLGSPLAKIGIELTDSPYVVASMRIMTRMGTSVLEALGDGEFIKCLHSVGCPLPLKKPLVNNWACNPELTLIAHLPDRREIISFGSGYGGNSLLGKKCFALRIASRLAKEEGWLAEHMLILGITNPEGKKKYLAAAFPSACGKTNLAMMNPTLPGWKVECVGDDIAWMKFDAQGNLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLAPGVTITSWKNKEWRPQDEEPCAHPNSRFCTPASQCPIIDPAWESPEGVPIEGIIFGGRRPAGVPLVYEALSWQHGVFVGAAMRSEATAAAEHKGKVIMHDPFAMRPFFGYNFGKYLAHWLSMAHRPAAKLPKIFHVNWFRKDKNGKFLWPGFGENSRVLEWMFGRIEGEDSAKLTPIGYVPKEDALNLKGLGDVNVEELFGISKEFWEKEVEEIDKYLEDQVNADLPYEIERELRALKQRISQM

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	brown rat,rat,rats
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	2-PHOSPHOGLYCOLIC ACID
Molecular weight formula_weight	156.0 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	BICARBONATE ION
Molecular weight formula_weight	61.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1544

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3dtba1
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	d3dtba2
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	d3dtbb1
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	d3dtbb2
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	3dtbA01
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	3dtbA02
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	3dtbA03
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	3dtbB01
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	3dtbB02
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	3dtbB03
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	62.154 Å
Unit-cell length b length_b	119.683 Å
Unit-cell length c length_c	86.849 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.05 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	28.830 Å
R factor r_factor	0.1690
R_work r_work	0.1680
R_free r_free	0.1930

The structure of rat cytosolic PEPCK in complex with phosphoglycolate and GDP

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

3dtb__assembly_1__model_1

3dtb__assembly_1__model_1 | I(q)

3dtb__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

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 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)

The structure of rat cytosolic PEPCK in complex with phosphoglycolate and GDP

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

3dtb__assembly_1__model_1

3dtb__assembly_1__model_1 | I(q)

3dtb__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

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 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)