3k8x

Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase in complex with tepraloxydim

Method: X-RAY DIFFRACTION

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

Acetyl-CoA carboxylase

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	(5S)-2-[(1E)-N-{[(2E)-3-chloroprop-2-en-1-yl]oxy}propanimidoyl]-3-hydroxy-5-(tetrahydro-2H-pyran-4-yl)cyclohex-2-en-1-one × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	(5S)-2-[(1E)-N-{[(2E)-3-chloroprop-2-en-1-yl]oxy}propanimidoyl]-3-hydroxy-5-(tetrahydro-2H-pyran-4-yl)cyclohex-2-en-1-one × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 3	(5S)-2-[(1E)-N-{[(2E)-3-chloroprop-2-en-1-yl]oxy}propanimidoyl]-3-hydroxy-5-(tetrahydro-2H-pyran-4-yl)cyclohex-2-en-1-one × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACAC_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–758； UniProt 1476–2233 Author chain B； PDBConstruct 1–758； UniProt 1476–2233 Author chain C； PDBConstruct 1–758； UniProt 1476–2233

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	3k8x
Deposition date deposition_date	2009-10-15
Structure title title	Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase in complex with tepraloxydim
Keywords keywords	;TRANSFERASE, ACETYL-COA CARBOXYLASE, CARBOXYLTRANSFERASE, ACC, CT, tepraloxydim, ATP-binding, Biotin, Fatty acid biosynthesis, Ligase, Lipid synthesis, Manganese, Metal-binding, Multifunctional enzyme, Nucleotide-binding, Phosphoprotein ;; 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.

3k8x__assembly_1__model_1

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

Download this curve (.dat)

3k8x__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3k8x__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.54 Å
Rg (electron density)	34.93 Å
Total Rg	35.44 Å
Atom count	11028
Residues	1376
Excluded volume	196360 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3k8x__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3k8x__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3k8x__assembly_3__model_1`	trimeric （3）	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	Acetyl-CoA carboxylase
Molecular weight formula_weight	85877.5 kDa
EC 编号 ec_number	6.4.1.2, 6.3.4.14
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	17693

GSMHLRPIATPYPVKEWLQPKRYKAHLMGTTYVYDFPELFRQASSSQWKNFSADVKLTDDFFISNELIEDENGELTEVEREPGANAIGMVAFKITVKTPEYPRGRQFVVVANDITFKIGSFGPQEDEFFNKVTEYARKRGIPRIYLAANSGARIGMAEEIVPLFQVAWNDAANPDKGFQYLYLTSEGMETLKKFDKENSVLTERTVINGEERFVIKTIIGSEDGLGVECLRGSGLIAGATSRAYHDIFTITLVTCRSVGIGAYLVRLGQRAIQVEGQPIILTGAPAINKMLGREVYTSNLQLGGTQIMYNNGVSHLTAVDDLAGVEKIVEWMSYVPAKRNMPVPILETKDTWDRPVDFTPTNDETYDVRWMIEGRETESGFEYGLFDKGSFFETLSGWAKGVVVGRARLGGIPLGVIGVETRTVENLIPADPANPNSAETLIQEPGQVWHPNSAFKTAQAINDFNNGEQLPMMILANWRGFSGGQRDMFNEVLKYGSFIVDALVDYKQPIIIYIPPTGELRGGSWVVVDPTINADQMEMYADVNARAGVLEPQGMVGIKFRREKLLDTMNRLDDKYRELRSQLSNKSLAPEVHQQISKQLADRERELLPIYGQISLQFADLHDRSSRMVAKGVISKELEWTEARRFFFWRLRRRLNEEYLIKRLSHQVGEASRLEKIARIRSWYPASVDHEDDRQVATWIEENYKTLDDKLKGLKLESFAQDLAKKIRSDHDNAIDGLSEVIKMLSTDDKEKLLKTLK

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(5S)-2-[(1E)-N-{[(2E)-3-chloroprop-2-en-1-yl]oxy}propanimidoyl]-3-hydroxy-5-(tetrahydro-2H-pyran-4-yl)cyclohex-2-en-1-one
Molecular weight formula_weight	341.8 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1303

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3k8xa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.4 — Biotin dependent carboxylase carboxyltransferase domain

Domain ID domain_id	d3k8xa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.4 — Biotin dependent carboxylase carboxyltransferase domain

Domain ID domain_id	d3k8xb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.4 — Biotin dependent carboxylase carboxyltransferase domain

Domain ID domain_id	d3k8xb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.4 — Biotin dependent carboxylase carboxyltransferase domain

Domain ID domain_id	d3k8xc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.4 — Biotin dependent carboxylase carboxyltransferase domain

Domain ID domain_id	d3k8xc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.4 — Biotin dependent carboxylase carboxyltransferase domain

CATH v4.4 (9 domains)

Domain ID domain_id	3k8xA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	3k8xA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	460 — ClpP/crotonase fold
Homologous superfamily homologous superfamily	10 — Biotin dependent carboxylase carboxyltransferase

Domain ID domain_id	3k8xA03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	3k8xB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	3k8xB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	460 — ClpP/crotonase fold
Homologous superfamily homologous superfamily	10 — Biotin dependent carboxylase carboxyltransferase

Domain ID domain_id	3k8xB03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	3k8xC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	3k8xC02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	460 — ClpP/crotonase fold
Homologous superfamily homologous superfamily	10 — Biotin dependent carboxylase carboxyltransferase

Domain ID domain_id	3k8xC03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

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Unit-cell length a length_a	247.303 Å
Unit-cell length b length_b	124.797 Å
Unit-cell length c length_c	145.369 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.32 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1890
R_work r_work	0.1870
R_free r_free	0.2210

Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase in complex with tepraloxydim

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

Acetyl-CoA carboxylase

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

3k8x__assembly_1__model_1

3k8x__assembly_1__model_1 | I(q)

3k8x__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) 15 domains

SCOP 2.08 (6 domains)

CATH v4.4 (9 domains)

7. Citations (1)

Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase in complex with tepraloxydim

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

Acetyl-CoA carboxylase

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

3k8x__assembly_1__model_1

3k8x__assembly_1__model_1 | I(q)

3k8x__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) 15 domains

SCOP 2.08 (6 domains)

CATH v4.4 (9 domains)

7. Citations (1)