SAXSdb — 1eeh

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

UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MURD_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–437； UniProt 1–437

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	1eeh
Deposition date deposition_date	2000-01-31
Structure title title	UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE
Keywords keywords	LIGASE, PEPTIDOGLYCAN SYNTHESIS, MURD, ADP-FORMING ENZYME; LIGASE
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.

1eeh__assembly_1__model_1

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

Download this curve (.dat)

1eeh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1eeh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.96 Å
Rg (electron density)	22.92 Å
Total Rg	23.69 Å
Atom count	3286
Residues	431
Excluded volume	58369 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1eeh__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE
Molecular weight formula_weight	46889.2 kDa
EC 编号 ec_number	6.3.2.9
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3472

ADYQGKNVVIIGLGLTGLSCVDFFLARGVTPRVMDTRMTPPGLDKLPEAVERHTGSLNDEWLMAADLIVASPGIALAHPSLSAAADAGIEIVGDIELFCREAQAPIVAITGSNGKSTVTTLVGEMAKAAGVNVGVGGNIGLPALMLLDDECELYVLELSSFQLETTSSLQAVAATILNVTEDHMDRYPFGLQQYRAAKLRIYENAKVCVVNADDALTMPIRGADERCVSFGVNMGDYHLNHQQGETWLRVKGEKVLNVKEMKLSGQHNYTNALAALALADAAGLPRASSLKALTTFTGLPHRFEVVLEHNGVRWINDSKATNVGSTEAALNGLHVDGTLHLLLGGDGKSADFSPLARYLNGDNVRLYCFGRDGAQLAALRPEVAEQTETMEQAMRLLAPRVQPGDMVLLSPACASLDQFKNFEQRGNEFARLAKELG

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE
Molecular weight formula_weight	750.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	186

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1eeha1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.5 — MurCD N-terminal domain
Superfamily Superfamily superfamily	c.5.1 — MurCD N-terminal domain
Family Family family	c.5.1.1 — MurCD N-terminal domain

Domain ID domain_id	d1eeha2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.59 — MurD-like peptide ligases, peptide-binding domain
Superfamily Superfamily superfamily	c.59.1 — MurD-like peptide ligases, peptide-binding domain
Family Family family	c.59.1.1 — MurCDEF C-terminal domain

Domain ID domain_id	d1eeha3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.72 — Ribokinase-like
Superfamily Superfamily superfamily	c.72.2 — MurD-like peptide ligases, catalytic domain
Family Family family	c.72.2.1 — MurCDEF

CATH v4.4 (3 domains)

Domain ID domain_id	1eehA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1eehA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	190 — Protein-Tyrosine Phosphatase; Chain A
Homologous superfamily homologous superfamily	20 — Mur ligase, C-terminal domain

Domain ID domain_id	1eehA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily	10 — Mur-like, catalytic domain

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Unit-cell length a length_a	58.840 Å
Unit-cell length b length_b	63.280 Å
Unit-cell length c length_c	114.910 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	13.000 Å
R factor r_factor	0.2260
R_work r_work	0.2190
R_free r_free	0.2650

UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE

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

UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE

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

1eeh__assembly_1__model_1

1eeh__assembly_1__model_1 | I(q)

1eeh__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (3)

UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE

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

UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE

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

1eeh__assembly_1__model_1

1eeh__assembly_1__model_1 | I(q)

1eeh__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (3)