SAXSdb — 7b60

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

UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase

Escherichia coli (strain K12)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	4-[(furan-2-yl)methyl]-1lambda~6~,4-thiazinane-1,1-dione × 2 DIMETHYL SULFOXIDE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	4-[(furan-2-yl)methyl]-1lambda~6~,4-thiazinane-1,1-dione × 1 DIMETHYL SULFOXIDE × 1 ISOPROPYL ALCOHOL × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MURE_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–496； UniProt 1–495 Author chain B； PDBConstruct 2–496； UniProt 1–495

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	7b60
Deposition date deposition_date	2020-12-07
Structure title title	Crystal structure of MurE from E.coli in complex with Z1269139261
Keywords keywords	;UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2, 6-diaminopimelate ligase cell wall biosynthesis ligase, drug target, Structural Genomics, Structural Genomics Consortium, SGC, BIOSYNTHETIC PROTEIN, fragment screening ;; BIOSYNTHETIC PROTEIN
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.

7b60__assembly_1__model_1

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

Download this curve (.dat)

7b60__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7b60__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.90 Å
Rg (electron density)	26.06 Å
Total Rg	26.77 Å
Atom count	3719
Residues	487
Excluded volume	65805 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7b60__assembly_1__model_1`	monomer （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7b60__assembly_2__model_1`	monomer （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 (5)

Entity 1 Entity 1 polymer

Description description	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase
Molecular weight formula_weight	53493.5 kDa
EC 编号 ec_number	6.3.2.13
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7584

SMADRNLRDLLAPWVPDAPSRALREMTLDSRVAAAGDLFVAVVGHQADGRRYIPQAIAQGVAAIIAEAKDEATDGEIREMHGVPVIYLSQLNERLSALAGRFYHEPSDNLRLVGVTGTNGKTTTTQLLAQWSQLLGEISAVMGTVGNGLLGKVIPTENTTGSAVDVQHELAGLVDQGATFCAMEVSSHGLVQHRVAALKFAASVFTNLSRDHLDYHGDMEHYEAAKWLLYSEHHCGQAIINADDEVGRRWLAKLPDAVAVSMEDHINPNCHGRWLKATEVNYHDSGATIRFSSSWGDGEIESHLMGAFNVSNLLLALATLLALGYPLADLLKTAARLQPVCGRMEVFTAPGKPTVVVDYAHTPDALEKALQAARLHCAGKLWCVFGCGGDRDKGKRPLMGAIAEEFADVAVVTDDNPRTEEPRAIINDILAGMLDAGHAKVMEGRAEAVTCAVMQAKENDVVLVAGKGHEDYQIVGNQRLDYSDRVTVARLLGVIA

Source Source

Source organism organism	Escherichia coli (strain K12)
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	4-[(furan-2-yl)methyl]-1lambda~6~,4-thiazinane-1,1-dione
Molecular weight formula_weight	215.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ISOPROPYL ALCOHOL
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	206

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	7b60A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — MurE/MurF, N-terminal domain

Domain ID domain_id	7b60A02
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

Domain ID domain_id	7b60A03
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	7b60B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — MurE/MurF, N-terminal domain

Domain ID domain_id	7b60B02
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

Domain ID domain_id	7b60B03
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

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Unit-cell length a length_a	58.249 Å
Unit-cell length b length_b	58.382 Å
Unit-cell length c length_c	74.027 Å
Unit-cell angle α angle_alpha	97.27 °
Unit-cell angle β angle_beta	91.53 °
Unit-cell angle γ angle_gamma	105.61 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.910 Å
Low-resolution limit resolution_low	73.280 Å
R factor r_factor	0.2174
R_work r_work	0.2161
R_free r_free	0.2419

Crystal structure of MurE from E.coli in complex with Z1269139261

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

UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate 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

7b60__assembly_1__model_1

7b60__assembly_1__model_1 | I(q)

7b60__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of MurE from E.coli in complex with Z1269139261

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

UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate 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

7b60__assembly_1__model_1

7b60__assembly_1__model_1 | I(q)

7b60__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)