2ppy

Crystal structure of Enoyl-CoA hydrates (gk_1992) from Geobacillus Kaustophilus HTA426

Method: X-RAY DIFFRACTION

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

Enoyl-CoA hydratase

Geobacillus kaustophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	DI(HYDROXYETHYL)ETHER × 6 1,2-ETHANEDIOL × 2 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	DI(HYDROXYETHYL)ETHER × 2 1,2-ETHANEDIOL × 1 water × 3	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 3	DI(HYDROXYETHYL)ETHER × 4 1,2-ETHANEDIOL × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5KYF9_GEOKA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–265； UniProt 1–265 Author chain B； PDBConstruct 1–265； UniProt 1–265 Author chain C； PDBConstruct 1–265； UniProt 1–265 Author chain D； PDBConstruct 1–265； UniProt 1–265 Author chain E； PDBConstruct 1–265； UniProt 1–265 Author chain F； PDBConstruct 1–265； UniProt 1–265

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	2ppy
Deposition date deposition_date	2007-05-01
Structure title title	Crystal structure of Enoyl-CoA hydrates (gk_1992) from Geobacillus Kaustophilus HTA426
Keywords keywords	;BETA-OXIDATION, COA, ENOYL-COA HYDRATASE, FATTY ACID METABOLISM, LYASE, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI ;; 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.

2ppy__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2ppy__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ppy__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	28.50 Å
Rg (electron density)	27.52 Å
Total Rg	28.11 Å
Atom count	6203
Residues	771
Excluded volume	111080 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ppy__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ppy__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2ppy__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 (4)

Entity 1 Entity 1 polymer

Description description	Enoyl-CoA hydratase
Molecular weight formula_weight	29918.1 kDa
EC 编号 ec_number	4.2.1.17
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	13511

MTAVETKKQYLTVFKEDGIAEIHLHINKSNSYDLEFYKEFNAAIDDIRFDPDIKVVIVMSDVPKFFSAGADINFLRSADPRFKTQFCLFCNETLDKIARSPQVYIACLEGHTVGGGLEMALACDLRFMGDEAGKIGLPEVSLGVLAGTGGTQRLARLIGYSRALDMNITGETITPQEALEIGLVNRVFPQAETRERTREYARKLANSATYAVSNIKLAIMNGKEMPLNVAIRYEGELQNLLFRSEDAKEGLSAFLEKRQPNWKGI

Source Source

Source organism organism	Geobacillus kaustophilus
NCBI taxonomy ID ncbi_taxonomy_id	235909
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1098

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2ppya_
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.14.1.0 — automated matches

Domain ID domain_id	d2ppyb_
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.14.1.0 — automated matches

Domain ID domain_id	d2ppyc_
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.14.1.0 — automated matches

Domain ID domain_id	d2ppyd_
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.14.1.0 — automated matches

Domain ID domain_id	d2ppye_
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.14.1.0 — automated matches

Domain ID domain_id	d2ppyf_
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.14.1.0 — automated matches

CATH v4.4 (12 domains)

Domain ID domain_id	2ppyA01
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	2ppyA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	12 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Lyase 2-enoyl-coa Hydratase, Chain A, domain 2

Domain ID domain_id	2ppyB01
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	2ppyB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	12 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Lyase 2-enoyl-coa Hydratase, Chain A, domain 2

Domain ID domain_id	2ppyC01
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	2ppyC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	12 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Lyase 2-enoyl-coa Hydratase, Chain A, domain 2

Domain ID domain_id	2ppyD01
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	2ppyD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	12 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Lyase 2-enoyl-coa Hydratase, Chain A, domain 2

Domain ID domain_id	2ppyE01
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	2ppyE02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	12 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Lyase 2-enoyl-coa Hydratase, Chain A, domain 2

Domain ID domain_id	2ppyF01
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	2ppyF02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	12 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Lyase 2-enoyl-coa Hydratase, Chain A, domain 2

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Unit-cell length a length_a	136.201 Å
Unit-cell length b length_b	137.345 Å
Unit-cell length c length_c	79.131 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	24

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.160 Å
Low-resolution limit resolution_low	39.630 Å
R factor r_factor	0.1760
R_work r_work	0.1760
R_free r_free	0.2190

Crystal structure of Enoyl-CoA hydrates (gk_1992) from Geobacillus Kaustophilus HTA426

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

Enoyl-CoA hydratase

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

2ppy__assembly_2__model_1

2ppy__assembly_2__model_1 | I(q)

2ppy__assembly_2__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of Enoyl-CoA hydrates (gk_1992) from Geobacillus Kaustophilus HTA426

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

Enoyl-CoA hydratase

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

2ppy__assembly_2__model_1

2ppy__assembly_2__model_1 | I(q)

2ppy__assembly_2__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (1)