SMTL ID : 6q11.1

Crystal structure of MurA from Clostridium difficile, mutation C116S, in the presence of URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x EPU: URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID(Non-covalent)

EPU.1: 22 residues within 4Å: Chain A: K.26, N.27, A.97, I.122, 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, R.400 Ligands: EDO.2 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:A.97, A:I.122 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:K.26, A:K.26, A:R.96, A:R.125, A:R.125, A:R.125, A:R.125, A:S.166, A:S.166, A:E.192, A:E.192, A:R.236, A:R.236, A:T.307, A:E.332, A:E.332 Salt bridges: A:K.26, A:R.125, A:R.125, A:R.400 EPU.5: 22 residues within 4Å: Chain B: K.26, N.27, A.97, I.122, 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, R.400 Ligands: EDO.6 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:A.97, B:I.122 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:K.26, B:K.26, B:R.96, B:R.125, B:R.125, B:R.125, B:R.125, B:S.166, B:S.166, B:E.192, B:E.192, B:R.236, B:R.236, B:T.307, B:E.332, B:E.332 Salt bridges: B:K.26, B:R.125, B:R.125, B:R.400 EPU.9: 22 residues within 4Å: Chain C: K.26, N.27, A.97, I.122, 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, R.400 Ligands: EDO.10 29 PLIP interactions: 29 interactions with chain C Hydrophobic interactions: C:A.97, C:I.122 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:K.26, C:K.26, C:R.96, C:R.125, C:R.125, C:R.125, C:R.125, C:S.166, C:S.166, C:E.192, C:E.192, C:R.236, C:T.307, C:E.332, C:E.332 Salt bridges: C:K.26, C:R.125, C:R.125, C:R.400 EPU.13: 22 residues within 4Å: Chain D: K.26, N.27, A.97, I.122, 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, R.400 Ligands: EDO.14 29 PLIP interactions: 29 interactions with chain D Hydrophobic interactions: D:A.97, D:I.122 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:K.26, D:K.26, D:R.96, D:R.125, D:R.125, D:R.125, D:R.125, D:S.166, D:S.166, D:E.192, D:E.192, D:R.236, D:T.307, D:E.332, D:E.332 Salt bridges: D:K.26, D:R.125, D:R.125, D:R.400

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

EDO.2: 6 residues within 4Å: Chain A: R.96, L.100, R.125, H.130, G.168 Ligands: EPU.1 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 A: E.191 Chain C: P.165, E.191, P.301, H.302 Ligands: EDO.11 No protein-ligand interaction detected (PLIP) EDO.6: 6 residues within 4Å: Chain B: R.96, L.100, R.125, H.130, G.168 Ligands: EPU.5 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.7: 6 residues within 4Å: Chain B: E.191 Chain D: P.165, E.191, P.301, H.302 Ligands: EDO.15 No protein-ligand interaction detected (PLIP) EDO.10: 6 residues within 4Å: Chain C: R.96, L.100, R.125, H.130, G.168 Ligands: EPU.9 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.11: 6 residues within 4Å: Chain A: P.165, E.191, P.301, H.302 Chain C: E.191 Ligands: EDO.3 No protein-ligand interaction detected (PLIP) EDO.14: 6 residues within 4Å: Chain D: R.96, L.100, R.125, H.130, G.168 Ligands: EPU.13 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 EDO.15: 6 residues within 4Å: Chain B: P.165, E.191, P.301, H.302 Chain D: E.191 Ligands: EDO.7 No protein-ligand interaction detected (PLIP)

4 x NA: SODIUM ION(Non-functional Binders)

NA.4: 5 residues within 4Å: Chain A: D.351, S.354 Chain B: D.351, S.354 Ligands: NA.8 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.351, A:S.354, B:D.351, B:D.351, B:S.354 NA.8: 5 residues within 4Å: Chain A: D.351, S.354 Chain B: D.351, S.354 Ligands: NA.4 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.351, A:S.354, A:S.354, B:D.351, B:S.354 NA.12: 5 residues within 4Å: Chain C: D.351, S.354 Chain D: D.351, S.354 Ligands: NA.16 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:D.351, C:S.354, D:S.354 NA.16: 5 residues within 4Å: Chain C: D.351, S.354 Chain D: D.351, S.354 Ligands: NA.12 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:D.351, C:S.354, D:S.354

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dopkins, B.J. et al., Crystal structure of MurA from Clostridium difficile, mutation C116S, in the presence of URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID. 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