SMTL ID : 9ir6.1

Crystal structure of UDP-N-acetylmuramic Acid L-alanine ligase (MurC) from Roseburia faecis in complex with UNAM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

homo-dimer

Ligands

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 7 residues within 4Å: Chain A: F.7, K.33, N.110, Y.111, G.159, H.160, S.161 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.33, A:N.110, A:G.159 EDO.3: 6 residues within 4Å: Chain A: A.390, D.391, F.422, P.423, S.424, F.425 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.391, A:D.391, A:F.422 Water bridges: A:Q.363 EDO.4: 5 residues within 4Å: Chain B: G.223, E.224, D.245, S.247, C.248 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.245, B:S.247, B:S.247 EDO.6: 5 residues within 4Å: Chain B: H.339, P.340, R.369, F.373, F.377 No protein-ligand interaction detected (PLIP)

2 x EPZ: (2R)-2-{[(2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoic acid(Non-covalent)

EPZ.2: 15 residues within 4Å: Chain A: G.17, G.19, G.20, I.21, S.22, D.41, A.42, Q.62, T.77, A.78, A.79, I.80, N.84, R.100, C.169 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.79, A:I.80 Hydrogen bonds: A:I.21, A:A.42, A:Q.62, A:Q.62, A:T.77, A:A.78, A:A.79, A:N.84, A:R.100 Water bridges: A:S.22, A:D.41, A:D.41, A:T.77 EPZ.5: 13 residues within 4Å: Chain B: G.17, G.19, G.20, I.21, D.41, A.42, Q.62, T.77, A.78, A.79, I.80, H.81, N.84 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:A.79, B:I.80 Hydrogen bonds: B:I.21, B:A.42, B:Q.62, B:Q.62, B:T.77, B:A.79, B:N.84 Water bridges: B:S.22, B:T.77, B:A.78 Salt bridges: B:H.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Du, Y. et al., Unusual MurC Ligase and Peptidoglycan Discovered in Lachnospiraceae Using a Fluorescent L-Amino Acid Based Selective Labeling Probe. Angew.Chem.Int.Ed.Engl. (2025)

Release Date

2025-04-09

Peptides

UDP-N-acetylmuramate--L-alanine ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

UDP-N-acetylmuramate--L-alanine ligase

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