SMTL ID : 9bn8.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 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 Ligands: SO4.3, SO4.4 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:F.162 Hydrogen bonds: A:G.15, A:L.16, A:T.17, A:T.37, A:T.37, 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:R.38, A:R.38, A:S.72, A:S.72, A:K.116, A:G.138, A:S.160, A:T.322, A:T.322, A:T.322, A:K.349 Salt bridges: A:R.38, A:K.116, A:H.184 pi-Cation interactions: A:R.38

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

01.2: 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

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

SO4.3: 7 residues within 4Å: Chain A: T.322, A.415, S.416, L.417, N.422, F.423 Ligands: UMA.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.416, A:S.416, A:L.417, A:F.423 SO4.4: 10 residues within 4Å: Chain A: T.111, G.112, K.116, S.160, S.161, D.183, H.184, Y.195, K.199 Ligands: UMA.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.111, A:S.161, A:Y.195, A:Y.195 Water bridges: A:K.116, A:K.116, A:N.323 Salt bridges: A:K.116, A:H.184, A:K.199 SO4.5: 7 residues within 4Å: Chain A: N.114, G.115, K.116, S.117, T.118, R.303, K.320 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.115, A:S.117, A:T.118 Water bridges: A:S.113, A:N.114, A:K.116, A:S.326 Salt bridges: A:R.303, A:K.320 SO4.6: 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 Water bridges: A:R.33, A:R.33 Salt bridges: A:R.33 SO4.7: 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 SO4.8: 5 residues within 4Å: Chain A: T.37, G.56, S.57, L.58, H.79 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.56, A:L.58 Salt bridges: A:H.79 SO4.9: 7 residues within 4Å: Chain A: L.164, T.167, S.168, S.169, L.170, R.201, E.204 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.167, A:L.170, A:L.170 Salt bridges: A:R.201 SO4.10: 2 residues within 4Å: Chain A: R.366, R.401 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.366, A:R.401 SO4.11: 3 residues within 4Å: Chain A: Q.425, N.428, R.432 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.425, A:N.428, A:R.432 SO4.12: 2 residues within 4Å: Chain A: R.201 Ligands: GOL.14 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.168, A:E.204 Salt bridges: A:R.201 SO4.13: 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

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 6 residues within 4Å: Chain A: I.92, E.165, T.166, T.167, R.201 Ligands: SO4.12 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:I.92, A:T.167, A:R.201 Water bridges: A:I.92, A:S.168, A:S.168, 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 inhibitor A19. 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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