SMTL ID : 3vcy.5 (4 other biounits)

Structure of MurA (UDP-N-acetylglucosamine enolpyruvyl transferase), from Vibrio fischeri in complex with substrate UDP-N-acetylglucosamine and the drug fosfomycin.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-tetramer

Ligands

4 x FFQ: [(1R)-1-hydroxypropyl]phosphonic acid(Covalent)

FFQ.1: 4 residues within 4Å: Chain A: C.116, R.121, R.398 Ligands: PO4.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.121, A:R.398, A:R.398 Water bridges: A:L.371 FFQ.6: 6 residues within 4Å: Chain B: R.92, C.116, R.121, D.370, R.398 Ligands: PO4.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.398, B:R.398 FFQ.11: 6 residues within 4Å: Chain C: R.92, G.115, C.116, R.121, R.398 Ligands: PO4.10 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.121, C:R.398, C:R.398 Water bridges: C:T.369, C:L.371 FFQ.16: 5 residues within 4Å: Chain D: R.92, C.116, A.117, R.121, R.398 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.121, D:R.398 Water bridges: D:R.92, D:R.92, D:R.398

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

UD1.2: 20 residues within 4Å: Chain A: K.23, N.24, W.96, A.120, R.121, P.122, V.123, D.124, L.125, H.126, S.163, V.164, G.165, T.305, D.306, I.328, F.329, R.332 Ligands: PO4.3, GOL.4 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:W.96, A:L.125 Hydrogen bonds: A:N.24, A:D.124, A:L.125, A:H.126, A:S.163, A:V.164, A:G.165, A:D.306, A:R.332 Water bridges: A:R.92, A:A.120, A:R.121, A:R.121, A:S.163, A:S.163, A:E.189, A:E.189, A:R.233, A:D.306, A:I.328, A:R.332 Salt bridges: A:R.121 UD1.5: 20 residues within 4Å: Chain B: K.23, N.24, W.96, A.120, R.121, P.122, V.123, D.124, L.125, H.126, S.163, V.164, G.165, T.305, D.306, I.328, F.329, R.332 Ligands: PO4.7, GOL.8 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:W.96 Hydrogen bonds: B:N.24, B:N.24, B:D.124, B:L.125, B:H.126, B:V.164, B:G.165, B:D.306, B:R.332 Water bridges: B:R.92, B:A.120, B:R.121, B:R.121, B:R.121, B:E.189, B:E.189, B:R.233, B:I.328, B:R.332, B:R.372 Salt bridges: B:R.121 UD1.9: 21 residues within 4Å: Chain C: K.23, N.24, W.96, A.120, R.121, P.122, V.123, D.124, L.125, H.126, V.162, S.163, V.164, G.165, T.305, D.306, I.328, F.329, R.332 Ligands: PO4.10, GOL.12 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:W.96 Hydrogen bonds: C:K.23, C:K.23, C:N.24, C:D.124, C:L.125, C:H.126, C:S.163, C:V.164, C:G.165, C:D.306, C:R.332 Water bridges: C:R.92, C:A.120, C:R.121, C:R.121, C:S.163, C:S.163, C:E.189, C:E.189, C:H.300, C:T.305, C:T.305, C:I.328, C:R.372 Salt bridges: C:R.121 UD1.13: 22 residues within 4Å: Chain D: K.23, N.24, W.96, A.120, R.121, P.122, V.123, D.124, L.125, H.126, K.161, V.162, S.163, V.164, G.165, T.305, D.306, I.328, F.329, R.332 Ligands: PO4.14, GOL.15 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:W.96 Hydrogen bonds: D:K.23, D:K.23, D:N.24, D:A.120, D:D.124, D:L.125, D:H.126, D:S.163, D:V.164, D:G.165, D:D.306, D:R.332 Water bridges: D:R.92, D:R.121, D:R.121, D:S.163, D:S.163, D:E.189, D:E.189, D:R.233, D:T.305, D:T.305, D:T.305, D:R.372 Salt bridges: D:R.121

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 6 residues within 4Å: Chain A: K.23, R.121, R.398 Ligands: FFQ.1, UD1.2, GOL.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.398 Salt bridges: A:K.23, A:R.121 PO4.7: 6 residues within 4Å: Chain B: K.23, R.121, R.398 Ligands: UD1.5, FFQ.6, GOL.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.398 Water bridges: B:R.92, B:R.121, B:R.121, B:R.372, B:R.398 Salt bridges: B:K.23, B:R.121 PO4.10: 7 residues within 4Å: Chain C: K.23, R.92, R.121, R.398 Ligands: UD1.9, FFQ.11, GOL.12 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.398 Water bridges: C:K.23, C:K.23, C:D.50 Salt bridges: C:K.23, C:R.121 PO4.14: 5 residues within 4Å: Chain D: K.23, R.121, R.398 Ligands: UD1.13, GOL.15 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:R.398 Water bridges: D:K.23, D:R.92, D:R.92, D:R.121, D:D.306 Salt bridges: D:K.23, D:R.121

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: R.92, A.93, I.95, W.96, R.121, H.126, G.165 Ligands: UD1.2, PO4.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.92, A:R.121, A:H.126 Water bridges: A:R.92, A:R.121 GOL.8: 9 residues within 4Å: Chain B: R.92, A.93, I.95, W.96, R.121, H.126, G.165 Ligands: UD1.5, PO4.7 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.92, B:W.96, B:R.121 Water bridges: B:R.121, B:G.165 GOL.12: 9 residues within 4Å: Chain C: R.92, A.93, I.95, W.96, R.121, H.126, G.165 Ligands: UD1.9, PO4.10 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.92, C:R.121, C:H.126 Water bridges: C:R.92, C:R.121 GOL.15: 9 residues within 4Å: Chain D: R.92, A.93, I.95, W.96, R.121, H.126, G.165 Ligands: UD1.13, PO4.14 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.92, D:R.121, D:H.126 Water bridges: D:R.92, D:R.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bensen, D.C. et al., Structure of MurA (UDP-N-acetylglucosamine enolpyruvyl transferase) from Vibrio fischeri in complex with substrate UDP-N-acetylglucosamine and the drug fosfomycin. Acta Crystallogr.,Sect.F (2012)

Release Date

2012-04-11

Peptides

UDP-N-acetylglucosamine 1-carboxyvinyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

UDP-N-acetylglucosamine 1-carboxyvinyltransferase

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