SMTL ID : 8dp2.1

Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from Pseudomonas aeruginosa PAO1 in complex with UMA (Uridine-5'-diphosphate-N-acetylmuramoyl-L-Alanine)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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: G.14, G.16, K.17, S.18, D.37, T.38, R.39, S.76, P.77, G.78, L.79, G.142, N.143, G.145, S.164, F.166, Q.167, H.188 Ligands: MG.2, SIN.7 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:F.166 Hydrogen bonds: A:K.17, A:S.18, A:T.38, A:T.38, A:R.39, A:S.76, A:S.76, A:G.78, A:N.143, A:N.143, A:N.143, A:Q.167 Water bridges: A:G.16, A:S.18, A:S.18, A:G.19, A:R.39, A:G.78, A:G.78, A:S.80, A:K.120, A:K.120, A:G.142, A:S.164, A:T.328, A:T.328 Salt bridges: A:K.120, A:H.188 pi-Cation interactions: A:R.39

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: K.120, D.187, H.188, K.202 Ligands: UMA.1, SIN.7 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.188, H2O.1, H2O.2, H2O.2, H2O.3

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: A.107, A.109, I.111, R.210 1 PLIP interactions: 1 interactions with chain A Water bridges: A:I.111 GOL.4: 6 residues within 4Å: Chain A: S.80, L.81, R.82, E.169, R.191, Y.192 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.81, A:R.82, A:R.191, A:R.191, A:R.191

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 7 residues within 4Å: Chain A: N.118, A.119, K.120, S.121, T.122, R.309, K.326 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:A.119, A:S.121, A:T.122 Water bridges: A:K.120, A:T.122, A:T.122 Salt bridges: A:R.309, A:K.326

1 x PE8: 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL(Non-covalent)

PE8.6: 12 residues within 4Å: Chain A: M.8, R.10, R.29, L.31, R.71, E.72, Y.74, R.95, L.102, R.105, E.106, D.172 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.10, A:R.10, A:R.29, A:R.29, A:R.95, A:R.105 Water bridges: A:I.96, A:D.172

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.7: 10 residues within 4Å: Chain A: H.188, T.328, K.357, A.425, S.426, L.427, N.432, F.433 Ligands: UMA.1, MG.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.427 Hydrogen bonds: A:T.328, A:S.426, A:F.433 Salt bridges: A:H.188, A:K.357

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.8: 2 residues within 4Å: Chain A: R.438, L.439 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.439 Salt bridges: A:R.438

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from Pseudomonas aeruginosa PAO1 in complex with UMA (Uridine-5'-diphosphate-N-acetylmuramoyl-L-Alanine). to be published

Release Date

2022-08-17

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UDP-N-acetylmuramoylalanine--D-glutamate ligase