9s8i

Crystal Structure of UDP-N-acetylmuramate-L-alanine ligase (MurC) from Pseudomonas aeruginosa in complex with compound OSA_001176 (WYH78)

Method: X-RAY DIFFRACTION

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

UDP-N-acetylmuramate--L-alanine ligase

Pseudomonas aeruginosa

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	(1R,2S)-1-({4-[(5-tert-butyl-1-methyl-1H-pyrazol-3-yl)amino]-1H-pyrazolo[3,4-d]pyrimidin-6-yl}amino)-2,3-dihydro-1H-inden-2-ol × 2 PHOSPHATE ION × 6 UNKNOWN LIGAND × 2 1,2-ETHANEDIOL × 15 DI(HYDROXYETHYL)ETHER × 2 DIMETHYL SULFOXIDE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MURC_PSEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–480； UniProt 1–480 Author chain B； PDBConstruct 1–480； UniProt 1–480

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	9s8i
Deposition date deposition_date	2025-08-05
Last revision last_revision	2025-09-17
Structure title title	Crystal Structure of UDP-N-acetylmuramate-L-alanine ligase (MurC) from Pseudomonas aeruginosa in complex with compound OSA_001176 (WYH78)
Keywords keywords	Dimer, Inhibitor, BIOSYNTHETIC PROTEIN; 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.

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9s8i__assembly_1__model_1`	dimeric （2）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	UDP-N-acetylmuramate--L-alanine ligase
Molecular weight formula_weight	52906.3 kDa
EC 编号 ec_number	6.3.2.8
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	7679

MVKEPNGVTRTMRRIRRIHFVGIGGAGMCGIAEVLLNLGYEVSGSDLKASAVTERLEKFGAQIFIGHQAENADGADVLVVSSAINRANPEVASALERRIPVVPRAEMLAELMRYRHGIAVAGTHGKTTTTSLIASVFAAGGLDPTFVIGGRLNAAGTNAQLGASRYLVAEADESDASFLHLQPMVAVVTNIDADHMATYGGDFNKLKKTFVEFLHNLPFYGLAVMCVDDPVVREILPQIARPTVTYGLSEDADVRAINIRQEGMRTWFTVLRPEREPLDVSVNMPGLHNVLNSLATIVIATDEGISDEAIVQGLSGFQGVGRRFQVYGELQVEGGSVMLVDDYGHHPREVAAVIKAIRGGWPERRLVMVYQPHRYTRTRDLYEDFVQVLGEANVLLLMEVYPAGEEPIPGADSRQLCHSIRQRGQLDPIYFERDADLAPLVKPLLRAGDILLCQGAGDVGGLAPQLIKNPLFAGKGGKGAAENLYFQ

Source Source

Source organism organism	Pseudomonas aeruginosa
NCBI taxonomy ID ncbi_taxonomy_id	287
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	(1R,2S)-1-({4-[(5-tert-butyl-1-methyl-1H-pyrazol-3-yl)amino]-1H-pyrazolo[3,4-d]pyrimidin-6-yl}amino)-2,3-dihydro-1H-inden-2-ol
Molecular weight formula_weight	418.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	UNKNOWN LIGAND
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	nat
Copy count entity_count	15

Entity 6 Entity 6 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

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

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	353

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Unit-cell length a length_a	60.579 Å
Unit-cell length b length_b	99.108 Å
Unit-cell length c length_c	192.556 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	8

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	88.280 Å
R factor r_factor	0.1910
R_work r_work	0.1884
R_free r_free	0.2393

Crystal Structure of UDP-N-acetylmuramate-L-alanine ligase (MurC) from Pseudomonas aeruginosa in complex with compound OSA_001176 (WYH78)

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

UDP-N-acetylmuramate--L-alanine 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

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

Crystal Structure of UDP-N-acetylmuramate-L-alanine ligase (MurC) from Pseudomonas aeruginosa in complex with compound OSA_001176 (WYH78)

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

UDP-N-acetylmuramate--L-alanine 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

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)