3v4x

The Biochemical and Structural Basis for Inhibition of Enterococcus faecalis HMG-CoA Synthase, mvaS, by Hymeglusin

Method: X-RAY DIFFRACTION

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

HMG-CoA synthase

Enterococcus faecalis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	(7R,12R,13R)-13-formyl-12,14-dihydroxy-3,5,7-trimethyltetradeca-2,4-dienoic acid × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	(7R,12R,13R)-13-formyl-12,14-dihydroxy-3,5,7-trimethyltetradeca-2,4-dienoic acid × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	(7R,12R,13R)-13-formyl-12,14-dihydroxy-3,5,7-trimethyltetradeca-2,4-dienoic acid × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	(7R,12R,13R)-13-formyl-12,14-dihydroxy-3,5,7-trimethyltetradeca-2,4-dienoic acid × 1 water × 1	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	(7R,12R,13R)-13-formyl-12,14-dihydroxy-3,5,7-trimethyltetradeca-2,4-dienoic acid × 2 water × 2	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	(7R,12R,13R)-13-formyl-12,14-dihydroxy-3,5,7-trimethyltetradeca-2,4-dienoic acid × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9FD71_ENTFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–388； UniProt 1–383 Author chain B； PDBConstruct 6–388； UniProt 1–383 Author chain C； PDBConstruct 6–388； UniProt 1–383 Author chain D； PDBConstruct 6–388； UniProt 1–383

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	3v4x
Deposition date deposition_date	2011-12-15
Structure title title	The Biochemical and Structural Basis for Inhibition of Enterococcus faecalis HMG-CoA Synthase, mvaS, by Hymeglusin
Keywords keywords	HYDROXYMETHYLGLUTARYL-CoA SYNTHASE, Hymeglusin covalent adduct, Transferase-Inhibitor complex; Transferase/Inhibitor
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.

3v4x__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3v4x__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3v4x__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	21.39 Å
Rg (electron density)	20.07 Å
Total Rg	21.01 Å
Atom count	5987
Residues	386
Excluded volume	53672 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3v4x__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3v4x__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3v4x__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3v4x__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3v4x__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3v4x__assembly_6__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 (3)

Entity 1 Entity 1 polymer

Description description	HMG-CoA synthase
Molecular weight formula_weight	42596.9 kDa
EC 编号 ec_number	2.3.3.10
Mutation mutation	A163S
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	25027

GSTGSMTIGIDKISFFVPPYYIDMTALAEARNVDPGKFHIGIGQDQMAVNPISQDIVTFAANAAEAILTKEDKEAIDMVIVGTESSIDESKAAAVVLHRLMGIQPFARSFEIKEACYGATAGLQLAKNHVALHPDKKVLVVAADIAKYGLNSGGEPTQGAGAVAMLVSSEPRILALKEDNVMLTQDIYDFWRPTGHPYPMVDGPLSNETYIQSFAQVWDEHKKRTGLDFADYDALAFHIPYTKMGKKALLAKISDQTEAEQERILARYEESIIYSRRVGNLYTGSLYLGLISLLENATTLTAGNQIGLFSYGSGAVAEFFTGELVAGYQNHLQKETHLALLDNRTELSIAEYEAMFAETLDTDIDQTLEDELKYSISAINNTVRSYRN

Source Source

Source organism organism	Enterococcus faecalis
NCBI taxonomy ID ncbi_taxonomy_id	1351
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(7R,12R,13R)-13-formyl-12,14-dihydroxy-3,5,7-trimethyltetradeca-2,4-dienoic acid
Molecular weight formula_weight	326.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1087

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d3v4xa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

Domain ID domain_id	d3v4xa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

Domain ID domain_id	d3v4xa3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3v4xb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

Domain ID domain_id	d3v4xb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

Domain ID domain_id	d3v4xb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3v4xc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

Domain ID domain_id	d3v4xc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

Domain ID domain_id	d3v4xc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3v4xd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

Domain ID domain_id	d3v4xd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

Domain ID domain_id	d3v4xd3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (8 domains)

Domain ID domain_id	3v4xA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	3v4xA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	3v4xB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	3v4xB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	3v4xC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	3v4xC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	3v4xD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	3v4xD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

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Unit-cell length a length_a	108.333 Å
Unit-cell length b length_b	52.756 Å
Unit-cell length c length_c	117.576 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.51 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.952 Å
Low-resolution limit resolution_low	48.020 Å
R factor r_factor	0.1755
R_work r_work	0.1707
R_free r_free	0.2182

The Biochemical and Structural Basis for Inhibition of Enterococcus faecalis HMG-CoA Synthase, mvaS, by Hymeglusin

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

HMG-CoA synthase

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

3v4x__assembly_3__model_1

3v4x__assembly_3__model_1 | I(q)

3v4x__assembly_3__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) 20 domains

SCOP 2.08 (12 domains)

CATH v4.4 (8 domains)

7. Citations (1)

The Biochemical and Structural Basis for Inhibition of Enterococcus faecalis HMG-CoA Synthase, mvaS, by Hymeglusin

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

HMG-CoA synthase

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

3v4x__assembly_3__model_1

3v4x__assembly_3__model_1 | I(q)

3v4x__assembly_3__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) 20 domains

SCOP 2.08 (12 domains)

CATH v4.4 (8 domains)

7. Citations (1)