SMTL ID : 4eou.1

Crystal structure of E. coli dihydrodipicolinate synthase with pyruvate and succinic semi-aldehyde bound in active site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 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 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.152, A:V.154, A:I.157, H2O.5, H2O.7 K.3: 4 residues within 4Å: Chain A: A.123, E.124, T.126, N.156 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.123, A:T.126, H2O.5 K.4: 4 residues within 4Å: Chain B: A.152, V.154, K.155, I.157 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:A.152, B:V.154, B:I.157 K.6: 4 residues within 4Å: Chain B: A.123, E.124, T.126, N.156 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.123, B:T.126, H2O.14 K.7: 4 residues within 4Å: Chain C: A.152, V.154, K.155, I.157 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:A.152, C:V.154, C:I.157, H2O.23, H2O.25 K.9: 4 residues within 4Å: Chain C: A.123, E.124, T.126, N.156 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:A.123, C:T.126, H2O.22 K.10: 4 residues within 4Å: Chain D: A.152, V.154, K.155, I.157 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:A.152, D:V.154, D:I.157 K.12: 4 residues within 4Å: Chain D: A.123, E.124, T.126, N.156 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:A.123, D:T.126, H2O.32

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: S.48, A.49, G.78, V.103, Y.106 Chain B: N.80, Y.107 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.48, A:S.48, A:G.78, B:N.80, B:N.80 Water bridges: A:G.78, A:V.103 GOL.5: 7 residues within 4Å: Chain A: N.80, Y.107 Chain B: S.48, A.49, G.78, V.103, Y.106 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.48, B:S.48, A:N.80, A:N.80 Water bridges: B:G.78, B:V.103 GOL.8: 7 residues within 4Å: Chain C: S.48, A.49, G.78, V.103, Y.106 Chain D: N.80, Y.107 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:S.48, C:S.48, C:G.78, D:N.80, D:N.80 Water bridges: C:G.78, C:V.103, D:Y.107 GOL.11: 7 residues within 4Å: Chain C: N.80, Y.107 Chain D: S.48, A.49, G.78, V.103, Y.106 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boughton, B.A. et al., The crystal structure of dihydrodipicolinate synthase from Escherichia coli with bound pyruvate and succinic acid semialdehyde: Unambiguous resolution of the stereochemistry of the condensation product. Proteins (2012)

Release Date

2012-04-25

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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