2fah

The structure of mitochondrial PEPCK, Complex with Mn and GDP

Method: X-RAY DIFFRACTION

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

Phosphoenolpyruvate carboxykinase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	GUANOSINE-5'-DIPHOSPHATE × 1 MALONIC ACID × 1 MANGANESE (II) ION × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	GUANOSINE-5'-DIPHOSPHATE × 1 MALONIC ACID × 2 MANGANESE (II) ION × 2 water × 1	Consistent with protein count
3	Other combination	Monomer	Protein 1 其他Polymer 1	beta-D-fructofuranose-(2-1)-6-O-octanoyl-alpha-D-glucopyranose × 1 GUANOSINE-5'-DIPHOSPHATE × 1 MALONIC ACID × 1 MANGANESE (II) ION × 2 water × 1	Consistent with protein count
4	Other combination	Monomer	Protein 1 其他Polymer 1	beta-D-fructofuranose-(2-1)-6-O-octanoyl-alpha-D-glucopyranose × 1 GUANOSINE-5'-DIPHOSPHATE × 1 MALONIC ACID × 1 MANGANESE (II) ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PPCKM_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–608； UniProt 34–640 Author chain B； PDBConstruct 1–608； UniProt 34–640 Author chain C； PDBConstruct 1–608； UniProt 34–640 Author chain D； PDBConstruct 1–608； UniProt 34–640

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	2fah
Deposition date deposition_date	2005-12-07
Structure title title	The structure of mitochondrial PEPCK, Complex with Mn and GDP
Keywords keywords	phosphoenolpyruvate carboxykinase, PEPCK, PCK, PEP, GDP, kinase, phosphoryl transfer, 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.

2fah__assembly_1__model_1

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

Download this curve (.dat)

2fah__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2fah__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.79 Å
Rg (electron density)	23.70 Å
Total Rg	24.51 Å
Atom count	4770
Residues	608
Excluded volume	84189 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2fah__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2fah__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2fah__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2fah__assembly_4__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 (6)

Entity 1 Entity 1 polymer

Description description	Phosphoenolpyruvate carboxykinase
Molecular weight formula_weight	67391.9 kDa
EC 编号 ec_number	4.1.1.32
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	20770

LSTSLSALPAAARDFVEEAVRLCRPREVLLCDGSEEEGKELLRGLQDDGVLHPLPKYDNCWLARTDPRDVARVESKTVLVTPEQSDAVPPPPPSGGPPQLGNWMSPNAFQAAVQERFPGCMAGRPLYVIPFSMGPPTSPLAKLGVQVTDSPYVVLSMRIMTRVGPAVLQRLDDDFVRCLHSVGRPLPLTEPLVSSWPCDPSRVLVAHIPSERRIVSFGSGYGGNSLLGKKCFALRIASRMAQQQGWLAEHMLILGVTSPSGEKRYMAAAFPSACGKTNLAMMTPSLPGWRIHCVGDDIAWMKFDDEGRLRAINPERGFFGVAPGTSSRTNPNAMATIARNTIFTNVGLRSDGGVYWDGLDEPTEPGVTYTSWLGKPWKHGDPEPCAHPNSRFCAPADQCPIMDPRWDDPEGVPIDAIIFGGRRPRGVPLVVEAFGWRHGVFMGSAMRSEATAAAEHKGGRLMHDPFAMRPFFGYNAGRYLEHWLSTGLRSNARLPRLFHVNWFLRDNEGRFVWPGFGHNARVLAWIFGRIQGRDTARPTPIGWVPKEGDLDLGGLPGVDYSQLFPMEKGFWEEECRQLREYYGENFGADLPRDVMAELEGLEERVRKM

Entity 2 Entity 2 branched

Description description	beta-D-fructofuranose-(2-1)-6-O-octanoyl-alpha-D-glucopyranose
Molecular weight formula_weight	468.5 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	MALONIC ACID
Molecular weight formula_weight	104.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1450

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2faha1
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.109.1.0 — automated matches

Domain ID domain_id	d2faha2
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.91.1.0 — automated matches

Domain ID domain_id	d2fahb1
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.109.1.0 — automated matches

Domain ID domain_id	d2fahb2
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.91.1.0 — automated matches

Domain ID domain_id	d2fahc1
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.109.1.0 — automated matches

Domain ID domain_id	d2fahc2
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.91.1.0 — automated matches

Domain ID domain_id	d2fahd1
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.109.1.0 — automated matches

Domain ID domain_id	d2fahd2
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.91.1.0 — automated matches

CATH v4.4 (12 domains)

Domain ID domain_id	2fahA01
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	2fahA02
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	2fahA03
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	2fahB01
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	2fahB02
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	2fahB03
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	2fahC01
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	2fahC02
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	2fahC03
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	2fahD01
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	2fahD02
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	2fahD03
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	74.595 Å
Unit-cell length b length_b	90.852 Å
Unit-cell length c length_c	103.339 Å
Unit-cell angle α angle_alpha	64.23 °
Unit-cell angle β angle_beta	73.74 °
Unit-cell angle γ angle_gamma	71.18 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.090 Å
Low-resolution limit resolution_low	32.810 Å
R factor r_factor	0.1891
R_work r_work	0.1867
R_free r_free	0.2337

The structure of mitochondrial PEPCK, Complex with Mn and GDP

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

Phosphoenolpyruvate carboxykinase

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

2fah__assembly_1__model_1

2fah__assembly_1__model_1 | I(q)

2fah__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)

The structure of mitochondrial PEPCK, Complex with Mn and GDP

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

Phosphoenolpyruvate carboxykinase

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

2fah__assembly_1__model_1

2fah__assembly_1__model_1 | I(q)

2fah__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)