SMTL ID : 5a5e.1

CRYSTAL STRUCTURE OF MURD LIGASE FROM ESCHERICHIA COLI

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

monomer

Ligands

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 5 residues within 4Å: Chain A: A.212, M.218, S.229, M.234, G.235 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.212 Hydrogen bonds: A:S.229, A:S.229

1 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 1 residues within 4Å: Chain A: H.309 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.309

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

SO4.3: 6 residues within 4Å: Chain A: G.111, K.115, S.159, S.160, Y.194, K.198 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.160, A:S.160 Water bridges: A:F.161 Salt bridges: A:K.115, A:K.198 SO4.4: 6 residues within 4Å: Chain A: T.321, A.414, S.415, L.416, N.421, F.422 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.415, A:F.422 SO4.5: 4 residues within 4Å: Chain A: S.264, G.265, Y.269, H.334 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.265, A:Y.269, A:Y.269, A:R.313, A:H.334 Water bridges: A:H.334 SO4.6: 3 residues within 4Å: Chain A: A.282, G.283, L.284 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.282 SO4.7: 3 residues within 4Å: Chain A: G.14, L.15, T.16 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.14, A:T.16, A:T.16 Water bridges: A:G.17 SO4.8: 7 residues within 4Å: Chain A: N.113, G.114, K.115, S.116, T.117, R.302, K.319 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.114, A:S.116, A:T.117 Water bridges: A:T.117, A:N.271, A:R.302, A:K.319 Salt bridges: A:R.302, A:K.319

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

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