SMTL ID : 3v4t.1 (1 other biounit)

E. cloacae C115D MURA liganded with UNAG

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

UD1.1: 21 residues within 4Å: Chain A: K.22, N.23, L.26, W.95, R.120, P.121, V.122, D.123, L.124, H.125, K.160, S.162, V.163, G.164, T.304, D.305, I.327, F.328, R.331 Ligands: EDO.6, EDO.7 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:L.26, A:W.95 Hydrogen bonds: A:N.23, A:R.120, A:D.123, A:L.124, A:H.125, A:S.162, A:V.163, A:G.164, A:E.188, A:D.305, A:R.331 Water bridges: A:R.120, A:R.120, A:R.120, A:R.120, A:S.162, A:S.162, A:H.299, A:T.304 Salt bridges: A:R.120, A:R.120 UD1.10: 21 residues within 4Å: Chain B: N.23, W.95, R.120, P.121, V.122, D.123, L.124, H.125, K.160, V.161, S.162, V.163, G.164, T.304, D.305, I.327, F.328, R.331 Ligands: ACT.11, EDO.12, EDO.13 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:W.95 Hydrogen bonds: B:N.23, B:R.120, B:D.123, B:L.124, B:H.125, B:S.162, B:V.163, B:G.164, B:D.305, B:R.331 Water bridges: B:R.120, B:R.120, B:E.188, B:T.304 Salt bridges: B:R.120 UD1.15: 22 residues within 4Å: Chain C: K.22, N.23, L.26, W.95, R.120, P.121, V.122, D.123, L.124, H.125, K.160, V.161, S.162, V.163, G.164, T.304, D.305, I.327, F.328, R.331 Ligands: ACT.17, EDO.18 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:L.26, C:W.95, C:L.124 Hydrogen bonds: C:N.23, C:R.120, C:D.123, C:L.124, C:H.125, C:S.162, C:V.163, C:G.164, C:D.305, C:R.331 Water bridges: C:R.120, C:R.120, C:R.120, C:R.120, C:S.162, C:S.162, C:E.188, C:T.304, C:T.304, C:T.304, C:D.305 Salt bridges: C:R.120, C:R.120 UD1.22: 23 residues within 4Å: Chain D: K.22, N.23, L.26, W.95, R.120, P.121, V.122, D.123, L.124, H.125, K.160, S.162, V.163, G.164, T.304, D.305, I.327, F.328, R.331 Ligands: EDO.25, EDO.26, EDO.27, EDO.31 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:L.26, D:W.95 Hydrogen bonds: D:N.23, D:R.120, D:D.123, D:L.124, D:H.125, D:S.162, D:V.163, D:G.164, D:D.305, D:R.331 Water bridges: D:R.91, D:R.91, D:T.304, D:D.305 Salt bridges: D:R.120

9 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 8 residues within 4Å: Chain A: Y.84, V.87, K.88, S.110, L.111, P.112, G.113 Chain D: R.340 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:Y.84, A:V.87 Hydrogen bonds: A:Y.84, A:G.113 Salt bridges: D:R.340 ACT.3: 4 residues within 4Å: Chain A: R.267, I.273, E.274, T.275 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.273, A:T.275, A:T.275 ACT.4: 5 residues within 4Å: Chain A: A.363, Q.364, T.386, V.388 Chain D: E.140 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.364 ACT.5: 3 residues within 4Å: Chain A: T.324, N.350 Chain C: E.348 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.350, C:E.348 ACT.11: 4 residues within 4Å: Chain B: T.326, I.327, E.329 Ligands: UD1.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.329, B:E.329 Salt bridges: B:K.160 ACT.16: 4 residues within 4Å: Chain C: P.256, D.257, G.276, E.277 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:D.257 Hydrogen bonds: C:D.257, C:D.257 ACT.17: 6 residues within 4Å: Chain C: K.160, V.161, P.298, I.327 Chain D: R.295 Ligands: UD1.15 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Salt bridges: D:R.295 Hydrophobic interactions: C:P.298, C:I.327 Hydrogen bonds: C:V.161 Water bridges: C:T.326 ACT.23: 4 residues within 4Å: Chain D: Q.7, G.8, T.10, N.412 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:N.412 Hydrogen bonds: D:N.412 ACT.24: 4 residues within 4Å: Chain D: Q.108, E.140, Y.142, K.144 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.108 Salt bridges: D:K.144

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

EDO.6: 7 residues within 4Å: Chain A: R.91, I.94, W.95, R.120, H.125, G.164 Ligands: UD1.1 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: V.161, V.163, E.188, P.298, I.327 Ligands: UD1.1 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: D.260, L.263, A.264, R.267 Chain B: H.155 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: D.193, N.196, Y.226, L.229, Q.255 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain B: R.91, A.92, W.95, R.120, H.125, G.164 Ligands: UD1.10 Ligand excluded by PLIP EDO.13: 8 residues within 4Å: Chain B: K.22, L.26, D.49, M.90, R.91, A.92, R.397 Ligands: UD1.10 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain B: V.192, D.193, N.196, Y.226, L.229, Q.255 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain C: A.92, W.95, R.120, H.125, G.164 Ligands: UD1.15 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain C: T.52, K.55, L.86, T.89 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain C: V.192, D.193, N.196, Y.226, Q.255 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain C: T.17, R.252, N.253 Ligand excluded by PLIP EDO.25: 8 residues within 4Å: Chain D: R.91, A.92, W.95, R.120, H.125, G.164 Ligands: UD1.22, EDO.31 Ligand excluded by PLIP EDO.26: 9 residues within 4Å: Chain D: K.22, L.26, D.49, R.91, A.92, L.370, R.397 Ligands: UD1.22, EDO.31 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain D: V.161, E.188, P.298, I.327 Ligands: UD1.22 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain D: I.244, E.358, K.359, L.360, I.382 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain D: R.150, L.175, A.176, E.177, V.218 Ligand excluded by PLIP EDO.30: 8 residues within 4Å: Chain A: R.340 Chain D: Y.84, V.87, K.88, S.110, L.111, P.112, G.113 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain D: K.22, R.120, L.370 Ligands: UD1.22, EDO.25, EDO.26 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, J.Y. et al., Functional Consequence of Covalent Reaction of Phosphoenolpyruvate with UDP-N-acetylglucosamine 1-Carboxyvinyltransferase (MurA). J.Biol.Chem. (2012)

Release Date

2012-03-07

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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