29ZM | pdb_000029zm

Crystal Structure of UDP-N-acetylmuramate-L-alanine ligase (MurC) from Pseudomonas aeruginosa in complex with compound OSA_001175 (WYH77)

PDB DOI: https://doi.org/10.2210/pdb29ZM/pdb

Classification: LIGASE
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2026-04-16 Released: 2026-05-06
Deposition Author(s): Quintanilla-Madronal, G., Lloyd, A.J., Wang, Y., Todd, M.H., Dowson, C.G., Diaz-Saez, L.
Funding Organization(s): Comunidad de Madrid

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.256 (Depositor), 0.259 (DCC)
R-Value Work:
0.192 (Depositor), 0.196 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of UDP-N-acetylmuramate-L-alanine ligase (MurC) from Pseudomonas aeruginosa in complex with compound OSA_001175 (WYH77)

Quintanilla-Madronal, G., Lloyd, A.J., Wang, Y., Todd, M.H., Dowson, C.G., Diaz-Saez, L.

To be published.

Macromolecule Content

Total Structure Weight: 106.51 kDa
Atom Count: 7,403
Modeled Residue Count: 914
Deposited Residue Count: 960
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylmuramate--L-alanine ligase	A, B	480	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: murC, PA4411 EC: 6.3.2.8
UniProt
Find proteins for Q9HW02 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HW02 Go to UniProtKB: Q9HW02
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HW02
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1J52 Query on A1J52 Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain G [auth A] MOL2 format, chain T [auth B] MOL2 format, chain G [auth A] mmCIF format, chain T [auth B] mmCIF format, chain G [auth A]	G [auth A], T [auth B]	(1~{R},2~{R})-1-[[4-[(5-~{tert}-butyl-1-methyl-pyrazol-3-yl)amino]-1~{H}-pyrazolo[3,4-d]pyrimidin-6-yl]amino]-2,3-dihydro-1~{H}-inden-2-ol C₂₂ H₂₆ N₈ O OTFLFRAEUDDJKT-CRAIPNDOSA-N		Interactions Focus chain G [auth A] Focus chain T [auth B] Interactions & Density Focus chain G [auth A] Focus chain T [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain P [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain P [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain P [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A], L [auth A], P [auth A], V [auth B], W [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth A] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth A] Focus chain V [auth B] Focus chain W [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain S [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain S [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], S [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain S [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain S [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain J [auth A] MOL2 format, chain X [auth B] MOL2 format, chain J [auth A] mmCIF format, chain X [auth B] mmCIF format, chain J [auth A]	J [auth A], X [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain X [auth B] Interactions & Density Focus chain J [auth A] Focus chain X [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain U [auth B] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain U [auth B] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] M [auth A] N [auth A] O [auth A] H [auth A], I [auth A], M [auth A], N [auth A], O [auth A], Q [auth A], R [auth A], U [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain U [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain U [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]