SMTL ID : 5a5f.1

CRYSTAL STRUCTURE OF MURD LIGASE FROM ESCHERICHIA COLI IN COMPLEX WITH UMA AND ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

UMA.1: 17 residues within 4Å: Chain A: G.12, G.14, L.15, T.16, D.35, T.36, R.37, S.71, P.72, G.73, G.137, N.138, G.140, S.159, F.161, Q.162, H.183 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:F.161 Hydrogen bonds: A:G.14, A:L.15, A:T.16, A:T.36, A:T.36, A:R.37, A:G.73, A:N.138, A:N.138, A:N.138, A:N.138, A:Q.162 Water bridges: A:T.16, A:T.16, A:R.37, A:R.37, A:S.71, A:S.71, A:K.115, A:K.115, A:G.137, A:S.159 Salt bridges: A:K.115, A:H.183 pi-Cation interactions: A:R.37

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 17 residues within 4Å: Chain A: S.112, N.113, G.114, K.115, S.116, T.117, E.157, N.178, H.267, N.271, R.302, F.303, D.317, K.319, A.320, S.325, A.328 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:G.114, A:K.115, A:S.116, A:T.117, A:T.117, A:E.157, A:N.178, A:N.271, A:N.271, A:K.319, A:S.325 Water bridges: A:K.115, A:K.115, A:S.116, A:S.116, A:N.268, A:T.270 Salt bridges: A:K.115, A:R.302, A:K.319, A:K.319 pi-Stacking: A:H.267, A:H.267

2 x MLI: MALONATE ION(Non-functional Binders)

MLI.3: 6 residues within 4Å: Chain A: T.321, A.414, S.415, L.416, N.421, F.422 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.414, A:L.416 Hydrogen bonds: A:T.321, A:S.415, A:F.422 Salt bridges: A:K.348 MLI.4: 3 residues within 4Å: Chain A: H.241, T.246, H.334 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.246 Water bridges: A:Q.266, A:Q.266, A:Q.266 Salt bridges: A:H.241, A:H.241, A:H.334, A:H.334

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sink, R. et al., Crystallographic Study of Peptidoglycan Biosynthesis Enzyme MurD: Domain Movement Revisited. PLoS ONE (2016)

Release Date

2016-04-13

Peptides

UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE