SMTL ID : 9dqw.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.183, H.184, K.199 Ligands: UMA.2, ANP.6 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.184, H2O.1, H2O.1, H2O.1, H2O.2

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

UMA.2: 22 residues within 4Å: Chain A: I.12, G.13, 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 Ligands: MG.1 31 PLIP interactions: 31 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.17, A:T.37, A:T.37, A:R.38, A:G.74, A:G.138, A:N.139, A:N.139, A:N.139, A:N.139, A:Q.163 Water bridges: 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:K.116, A:S.160, A:N.323, A:K.349 Salt bridges: A:K.116, A:H.184 pi-Cation interactions: A:R.38

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

CL.3: 3 residues within 4Å: Chain A: A.415, S.416, F.423 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: N.241, R.250, K.255 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: D.3, Y.4, Q.5, R.28 Ligand excluded by PLIP

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.6: 20 residues within 4Å: Chain A: S.113, N.114, G.115, K.116, S.117, T.118, E.158, N.179, H.268, N.272, R.303, D.318, K.320, A.321, T.322, N.323, S.326, A.329 Ligands: MG.1, SO4.10 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:N.114, A:N.114, A:G.115, A:K.116, A:K.116, A:S.117, A:S.117, A:T.118, A:T.118, A:N.179, A:H.268, A:H.268, A:N.272, A:N.272, A:R.303, A:R.303, A:T.322, A:T.322, A:N.323, A:S.326 Water bridges: A:S.117, A:S.117, A:D.183, A:N.269 pi-Stacking: A:H.268, A:H.268

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.7: 5 residues within 4Å: Chain A: M.39, T.40, L.44, R.53, T.55 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.53

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 1 residues within 4Å: Chain A: Q.171 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.171 GOL.9: 3 residues within 4Å: Chain A: H.239, R.250, G.253 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.250

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

SO4.10: 8 residues within 4Å: Chain A: N.114, G.115, K.116, S.117, T.118, R.303, K.320 Ligands: ANP.6 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.115, A:S.117, A:S.117, A:T.118, A:T.118 Water bridges: A:K.116, A:K.116, A:S.117, A:S.117, A:N.272, A:R.303 SO4.11: 3 residues within 4Å: Chain A: E.309, H.310, N.311 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.309, A:N.311 Water bridges: A:V.313 Salt bridges: A:H.310

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seibold, S. et al., Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli in complex with UMA and AMP-PNP. To be published

Release Date

2024-10-09

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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