SMTL ID : 3du0.1

E. coli dihydrodipicolinate synthase with first substrate, pyruvate, bound in active site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

8 x K: POTASSIUM ION(Non-covalent)

K.1: 4 residues within 4Å: Chain A: A.152, V.154, K.155, I.157 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:A.152, A:V.154, A:I.157 K.2: 4 residues within 4Å: Chain A: S.48, A.49, L.51 Ligands: GOL.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.48, A:A.49, A:L.51, H2O.4 K.7: 4 residues within 4Å: Chain B: A.152, V.154, K.155, I.157 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.152, B:V.154, B:I.157, H2O.17 K.8: 4 residues within 4Å: Chain B: S.48, A.49, L.51 Ligands: GOL.4 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.48, B:A.49, B:L.51, H2O.4, H2O.15 K.12: 4 residues within 4Å: Chain C: A.152, V.154, K.155, I.157 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:A.152, C:V.154, C:I.157 K.13: 4 residues within 4Å: Chain C: S.48, A.49, L.51 Ligands: GOL.15 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.48, C:A.49, C:L.51, H2O.24 K.18: 4 residues within 4Å: Chain D: A.152, V.154, K.155, I.157 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:A.152, D:V.154, D:I.157, H2O.37 K.19: 4 residues within 4Å: Chain D: S.48, A.49, L.51 Ligands: GOL.15 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.48, D:A.49, D:L.51, H2O.24, H2O.35

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: S.48, A.49, G.78, V.103, Y.106 Chain B: N.80, Y.107 Ligands: GOL.4 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:N.80, B:N.80, A:S.48 Water bridges: B:Y.107, A:S.48, A:G.78, A:G.78, A:V.103 GOL.4: 9 residues within 4Å: Chain A: A.49, N.80, Y.106 Chain B: N.80, Y.106 Ligands: K.2, GOL.3, K.8, GOL.9 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:A.49, A:N.80, A:Y.106, B:N.80, B:Y.106 Water bridges: A:N.80, B:S.48, B:N.80 GOL.9: 8 residues within 4Å: Chain A: N.80, Y.107 Chain B: S.48, A.49, G.78, V.103, Y.106 Ligands: GOL.4 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:N.80, A:N.80, B:S.48, B:S.48 Water bridges: B:G.78, B:V.103 GOL.14: 8 residues within 4Å: Chain C: S.48, A.49, G.78, V.103, Y.106 Chain D: N.80, Y.107 Ligands: GOL.15 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:S.48, D:N.80, D:N.80 Water bridges: C:S.48, C:H.56, C:G.78, C:G.78, C:V.103, D:Y.107 GOL.15: 9 residues within 4Å: Chain C: A.49, N.80, Y.106 Chain D: N.80, Y.106 Ligands: K.13, GOL.14, K.19, GOL.20 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:N.80, C:A.49, C:N.80, C:Y.106, C:Y.106 Water bridges: D:S.48, D:N.80, C:N.80 GOL.20: 8 residues within 4Å: Chain C: N.80, Y.107 Chain D: S.48, A.49, G.78, V.103, Y.106 Ligands: GOL.15 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.48, D:S.48, C:N.80, C:N.80 Water bridges: D:G.78, D:V.103

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 5 residues within 4Å: Chain A: V.135, P.136, S.137, A.163, T.164 Ligand excluded by PLIP CL.6: 7 residues within 4Å: Chain A: N.166, L.167, T.168 Chain C: G.165, N.166, L.167 Ligands: CL.17 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain B: N.166, L.167 Chain D: G.165, N.166, L.167 Ligands: CL.21 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain B: V.135, P.136, S.137, A.163, T.164 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain C: V.135, P.136, S.137, A.163, T.164 Ligand excluded by PLIP CL.17: 7 residues within 4Å: Chain A: G.165, N.166, L.167 Chain C: N.166, L.167, T.168 Ligands: CL.6 Ligand excluded by PLIP CL.21: 6 residues within 4Å: Chain B: G.165, N.166, L.167 Chain D: N.166, L.167 Ligands: CL.10 Ligand excluded by PLIP CL.22: 5 residues within 4Å: Chain D: V.135, P.136, S.137, A.163, T.164 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Devenish, S.R. et al., The high-resolution structure of dihydrodipicolinate synthase from Escherichia coli bound to its first substrate, pyruvate. Acta Crystallogr.,Sect.F (2008)

Release Date

2008-11-18

Peptides

Dihydrodipicolinate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Dihydrodipicolinate synthase

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