SMTL ID : 6q0y.1

Crystal structure of MurA from Clostridium difficile, mutant C116S, in the presence of Uridine-Diphosphate-N-Acetylglucosamine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: R.96, L.100, R.125, H.130, G.168 Ligands: UD1.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.96, A:R.96, A:R.125, A:H.130 Water bridges: A:G.168 EDO.3: 6 residues within 4Å: Chain B: R.96, L.100, R.125, H.130, G.168 Ligands: UD1.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.96, B:R.96, B:R.125, B:H.130 Water bridges: B:G.168 EDO.5: 6 residues within 4Å: Chain C: R.96, L.100, R.125, H.130, G.168 Ligands: UD1.6 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.96, C:R.96, C:R.125, C:H.130 Water bridges: C:G.168 EDO.7: 6 residues within 4Å: Chain D: R.96, L.100, R.125, H.130, G.168 Ligands: UD1.8 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.96, D:R.96, D:R.125, D:H.130 Water bridges: D:G.168

4 x UD1: URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE(Non-covalent)

UD1.2: 19 residues within 4Å: Chain A: 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 Ligands: EDO.1 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:A.97 Hydrogen bonds: A:N.27, A:D.128, A:L.129, A:H.130, A:S.166, A:V.167, A:G.168, A:D.308, A:R.334 Water bridges: A:K.26, A:K.26, A:R.96, A:T.124, 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 Salt bridges: A:R.125 UD1.4: 19 residues within 4Å: Chain B: 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 Ligands: EDO.3 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:A.97 Hydrogen bonds: B:N.27, B:D.128, B:L.129, B:H.130, B:S.166, B:V.167, B:G.168, B:D.308, B:R.334 Water bridges: B:K.26, B:K.26, B:R.96, B:T.124, 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 Salt bridges: B:R.125 UD1.6: 19 residues within 4Å: Chain C: 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 Ligands: EDO.5 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:A.97 Hydrogen bonds: C:N.27, C:D.128, C:L.129, C:H.130, C:S.166, C:V.167, C:G.168, C:D.308, C:R.334 Water bridges: C:K.26, C:K.26, C:R.96, C:T.124, 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 Salt bridges: C:R.125 UD1.8: 19 residues within 4Å: Chain D: 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 Ligands: EDO.7 24 PLIP interactions: 24 interactions with chain D Hydrophobic interactions: D:A.97 Hydrogen bonds: D:N.27, D:D.128, D:L.129, D:H.130, D:S.166, D:V.167, D:G.168, D:D.308, D:R.334 Water bridges: D:K.26, D:K.26, D:R.96, D:T.124, 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 Salt bridges: D:R.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dopkins, B.J. et al., Crystal structure of MurA from Clostridium difficile, mutant C116S, in the presence of Uridine-Diphosphate-N-Acetylglucosamine. 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