SMTL ID : 6q03.1

Crystal structure of MurA from Clostridium difficile in the presence of UDP-N-acetyl-alpha-D-muramic acid with modified Cys116 (S-[(1S)-1-carboxy-1-(phosphonooxy)ethyl]-L-cysteine)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x EPZ: (2R)-2-{[(2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoic acid(Non-covalent)

EPZ.1: 21 residues within 4Å: Chain A: K.26, N.27, A.97, T.124, R.125, P.126, I.127, D.128, L.129, H.130, F.164, S.166, V.167, G.168, T.307, D.308, V.330, F.331, R.334, L.373 Ligands: EDO.2 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:A.97 Hydrogen bonds: A:N.27, A:D.128, A:L.129, A:H.130, A:V.167, A:G.168, A:D.308, A:R.334 Water bridges: A:T.124, A:R.125, A:R.125, A:R.125, A:R.125, A:R.125, A:S.166, A:S.166, A:E.192, A:R.236, A:R.236, A:T.307, A:E.332, A:E.332, A:R.400, A:R.400 Salt bridges: A:K.26, A:R.125, A:R.400 EPZ.3: 21 residues within 4Å: Chain B: K.26, N.27, A.97, T.124, R.125, P.126, I.127, D.128, L.129, H.130, F.164, S.166, V.167, G.168, T.307, D.308, V.330, F.331, R.334, L.373 Ligands: EDO.4 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:A.97 Hydrogen bonds: B:N.27, B:D.128, B:L.129, B:H.130, B:V.167, B:G.168, B:D.308, B:R.334 Water bridges: B:T.124, B:R.125, B:R.125, B:R.125, B:R.125, B:R.125, B:S.166, B:S.166, B:E.192, B:R.236, B:R.236, B:T.307, B:E.332, B:E.332, B:R.400, B:R.400 Salt bridges: B:K.26, B:R.125, B:R.400 EPZ.5: 21 residues within 4Å: Chain C: K.26, N.27, A.97, T.124, R.125, P.126, I.127, D.128, L.129, H.130, F.164, S.166, V.167, G.168, T.307, D.308, V.330, F.331, R.334, L.373 Ligands: EDO.6 27 PLIP interactions: 27 interactions with chain C Hydrophobic interactions: C:A.97 Hydrogen bonds: C:N.27, C:D.128, C:L.129, C:H.130, C:V.167, C:G.168, C:D.308, C:R.334 Water bridges: C:T.124, C:R.125, C:R.125, C:R.125, C:R.125, C:R.125, C:S.166, C:S.166, C:E.192, C:R.236, C:R.236, C:T.307, C:E.332, C:R.400, C:R.400 Salt bridges: C:K.26, C:R.125, C:R.400 EPZ.7: 21 residues within 4Å: Chain D: K.26, N.27, A.97, T.124, R.125, P.126, I.127, D.128, L.129, H.130, F.164, S.166, V.167, G.168, T.307, D.308, V.330, F.331, R.334, L.373 Ligands: EDO.8 27 PLIP interactions: 27 interactions with chain D Hydrophobic interactions: D:A.97 Hydrogen bonds: D:N.27, D:D.128, D:L.129, D:H.130, D:V.167, D:G.168, D:D.308, D:R.334 Water bridges: D:T.124, D:R.125, D:R.125, D:R.125, D:R.125, D:R.125, D:S.166, D:S.166, D:E.192, D:R.236, D:R.236, D:T.307, D:E.332, D:R.400, D:R.400 Salt bridges: D:K.26, D:R.125, D:R.400

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: R.96, A.97, L.100, R.125, H.130, G.168 Ligands: EPZ.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.125, A:H.130 Water bridges: A:R.125, A:G.168, A:G.168 EDO.4: 7 residues within 4Å: Chain B: R.96, A.97, L.100, R.125, H.130, G.168 Ligands: EPZ.3 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.125, B:H.130 Water bridges: B:R.125, B:G.168, B:G.168 EDO.6: 7 residues within 4Å: Chain C: R.96, A.97, L.100, R.125, H.130, G.168 Ligands: EPZ.5 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.125, C:H.130 Water bridges: C:R.125, C:G.168, C:G.168 EDO.8: 7 residues within 4Å: Chain D: R.96, A.97, L.100, R.125, H.130, G.168 Ligands: EPZ.7 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.125, D:H.130 Water bridges: D:R.125, D:G.168, D:G.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dopkins, B.J. et al., Crystal structure of MurA from Clostridium difficile in the presence of UDP-N-acetyl-alpha-D-muramic acid with modified Cys116 (S-[(1S)-1-carboxy-1-(phosphonooxy)ethyl]-L-cysteine). To Be Published

Release Date

2019-11-27

Peptides

UDP-N-acetylglucosamine 1-carboxyvinyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

UDP-N-acetylglucosamine 1-carboxyvinyltransferase