SMTL ID : 5t26.1

Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase from Escherichia coli.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: L.245, N.250, P.251, P.253, V.254 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.250, A:V.254 NA.2: 7 residues within 4Å: Chain A: V.12, T.13, T.47, G.48, E.49, P.251, K.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.13, A:G.48 NA.3: 6 residues within 4Å: Chain A: S.7, T.38, A.209, A.213, M.216, A.217 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.7, A:S.7, A:A.217 NA.4: 8 residues within 4Å: Chain A: P.107, Y.108, Y.109, N.110, R.111, P.112, T.141, C.143 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.107, A:Y.109, A:R.111 NA.5: 4 residues within 4Å: Chain A: S.187, D.189, S.192, F.196 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.192 NA.6: 7 residues within 4Å: Chain B: V.12, T.13, T.47, G.48, E.49, P.251, K.255 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.13, B:K.255 NA.7: 5 residues within 4Å: Chain B: L.245, N.250, P.251, P.253, V.254 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.251, B:V.254 NA.10: 5 residues within 4Å: Chain C: L.245, N.250, P.251, P.253, V.254 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.245, C:V.254 NA.11: 7 residues within 4Å: Chain C: V.12, T.13, T.47, G.48, E.49, P.251, K.255 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.13, C:T.47, C:E.49 NA.12: 6 residues within 4Å: Chain C: S.7, T.38, A.209, A.213, M.216, A.217 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.7, C:A.213, C:A.217 NA.13: 8 residues within 4Å: Chain C: P.107, Y.108, Y.109, N.110, R.111, P.112, T.141, C.143 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.109, C:R.111, C:T.141 NA.14: 4 residues within 4Å: Chain C: S.187, D.189, S.192, F.196 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.189 NA.15: 7 residues within 4Å: Chain D: V.12, T.13, T.47, G.48, E.49, P.251, K.255 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.13, D:G.48, D:E.49 NA.16: 5 residues within 4Å: Chain D: L.245, N.250, P.251, P.253, V.254 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:P.251, D:V.254

2 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.8: 5 residues within 4Å: Chain B: G.226, H.227, F.228, A.229, E.230 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:A.229, B:E.230 Water bridges: B:G.226, B:G.226, B:H.227, B:F.228, B:F.228 TLA.17: 5 residues within 4Å: Chain D: G.226, H.227, F.228, A.229, E.230 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:A.229, D:E.230, D:E.230 Water bridges: D:G.226, D:G.226, D:H.227, D:F.228, D:F.228

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 7 residues within 4Å: Chain B: S.50, A.51, G.80, V.105, Y.108 Chain D: N.82, Y.109 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:N.82, D:N.82, D:Y.109, B:S.50, B:S.50 GOL.18: 7 residues within 4Å: Chain B: N.82, Y.109 Chain D: S.50, A.51, G.80, V.105, Y.108 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:S.50, D:S.50, B:N.82, B:N.82, B:Y.109 Water bridges: D:Y.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chooback, L. et al., Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase from Escherichia coli. To Be Published

Release Date

2016-10-05

Peptides

4-hydroxy-tetrahydrodipicolinate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

4-hydroxy-tetrahydrodipicolinate synthase

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