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2y66

New 5-Benzylidenethiazolidine-4-one Inhibitors of Bacterial MurD Ligase: Design, Synthesis, Crystal Structures, and Biological Evaluation

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE

ESCHERICHIA COLI

UniProt P14900

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 (2R)-2-[[3-[[3-[(Z)-(2,4-dioxo-1,3-thiazolidin-5-ylidene)methyl]phenoxy]methyl]phenyl]carbonylamino]pentanedioic acid × 1 DIMETHYL SULFOXIDE × 1 SULFATE ION × 1 SULFITE ION × 1 CHLORIDE ION × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1e0d 1eeh 1uag 2jff 2jfg 2jfh 2uag 2uuo 2uup 2vtd 2vte 2wjp

30 assemblies; showing the first 12

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name MURD_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–438； UniProt 1–438

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_id2y66
Deposition date deposition_date2011-01-20
Structure title titleNew 5-Benzylidenethiazolidine-4-one Inhibitors of Bacterial MurD Ligase: Design, Synthesis, Crystal Structures, and Biological Evaluation
Keywords keywords;ATP-BINDING, CELL CYCLE, CELL DIVISION, CELL SHAPE, CELL WALL BIOGENESIS/DEGRADATION, LIGASE, NUCLEOTIDE-BINDING, PEPTIDOGLYCAN SYNTHESIS, UMA ;; LIGASE
Experimental Method methodX-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.

2y66__assembly_1__model_1

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

Download this curve (.dat)

2y66__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2y66__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）23.57 Å
Rg (electron density)22.50 Å
Total Rg23.25 Å
Atom count3315
Residues433
Excluded volume58845 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2y66__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 (7)

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id2y66A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id2y66A02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily10 — Mur-like, catalytic domain
Domain ID domain_id2y66A03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology190 — Protein-Tyrosine Phosphatase; Chain A
Homologous superfamily homologous superfamily20 — Mur ligase, C-terminal domain
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7. Citations (1)