SMTL ID : 9bn9.1

Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli in complex with UMA and two inhibitor A19 molecules

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.23 Å

Oligo State

monomer

Ligands

1 x UMA: URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE(Non-covalent)

UMA.1: 20 residues within 4Å: Chain A: I.12, G.15, L.16, T.17, D.36, T.37, R.38, S.72, P.73, G.74, I.75, G.138, N.139, G.141, S.160, F.162, Q.163, H.184, L.417, F.423 35 PLIP interactions: 35 interactions with chain A Hydrophobic interactions: A:F.162, A:F.423 Hydrogen bonds: A:G.15, A:L.16, A:T.17, A:T.37, A:T.37, A:S.72, A:G.74, A:G.74, A:N.139, A:N.139, A:N.139, A:N.139, A:Q.163 Water bridges: A:T.17, A:T.17, A:T.37, A:R.38, A:R.38, A:R.38, A:S.72, A:S.72, A:K.116, A:K.116, A:G.138, A:S.160, A:R.187, A:T.322, A:T.322, A:N.323, A:K.349 Salt bridges: A:R.38, A:K.116, A:H.184

2 x 01: N-(4-{[(4S)-3-amino[1,2,4]triazolo[4,3-b]pyridazin-6-yl]sulfanyl}phenyl)acetamide

01.2: 7 residues within 4Å: Chain A: P.106, Q.171, A.172, V.173, N.205, A.206, K.207 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.106, A:Q.171 Hydrogen bonds: A:Q.171, A:N.205 Water bridges: A:Q.171 01.3: 3 residues within 4Å: Chain A: F.190, Q.193, Q.194 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.193 pi-Stacking: A:F.190, A:F.190 pi-Cation interactions: A:F.190

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 7 residues within 4Å: Chain A: N.114, G.115, K.116, S.117, T.118, R.303, K.320 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.115, A:S.117, A:T.118 Water bridges: A:N.114, A:K.116, A:K.320, A:K.320, A:S.326 Salt bridges: A:R.303, A:K.320 SO4.5: 3 residues within 4Å: Chain A: N.8, R.33, A.65 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.8, A:R.33 Water bridges: A:R.33, A:R.33 SO4.6: 3 residues within 4Å: Chain A: R.38, M.39, T.40 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.39, A:T.40 SO4.7: 8 residues within 4Å: Chain A: L.164, T.167, S.168, S.169, L.170, R.201, E.204 Ligands: CL.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.167, A:L.170, A:L.170 Salt bridges: A:R.201 SO4.8: 2 residues within 4Å: Chain A: Q.425, N.428 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.425, A:N.428 SO4.9: 3 residues within 4Å: Chain A: H.310, N.311, G.439 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.311, A:N.311 Salt bridges: A:H.310

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 1 residues within 4Å: Chain A: S.416 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: T.167, S.168, S.169, L.170 Ligands: SO4.7 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 5 residues within 4Å: Chain A: L.77, I.92, E.165, T.166, R.201 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.92 Water bridges: A:S.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, L. et al., Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli in complex with UMA and two inhibitor A19 molecules. To be published

Release Date

2024-05-15

Peptides

UDP-N-acetylmuramoylalanine--D-glutamate ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UDP-N-acetylmuramoylalanine--D-glutamate ligase

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