SMTL ID : 3c0j.1 (1 other biounit)

Structure of E. coli dihydrodipicolinate synthase complexed with hydroxypyruvate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 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.4, H2O.9 K.5: 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.8: 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.22, H2O.27 K.12: 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

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: A.49, N.80, Y.106 Chain B: N.80, Y.106 Ligands: GOL.3, GOL.4 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:A.49, B:Y.106 Water bridges: A:H.53, A:N.80, A:Y.106, B:S.48, B:A.49, B:N.80 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.2 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.48, A:S.48, A:G.78, B:N.80 Water bridges: A:G.78, A:Y.106 GOL.4: 8 residues within 4Å: Chain A: N.80, Y.107 Chain B: S.48, A.49, G.78, V.103, Y.106 Ligands: GOL.2 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.48, A:N.80, A:N.80 Water bridges: B:S.48, B:G.78, B:G.78, B:V.103, A:Y.107 GOL.9: 7 residues within 4Å: Chain C: A.49, N.80, Y.106 Chain D: N.80, Y.106 Ligands: GOL.10, GOL.11 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:A.49, C:Y.106 Water bridges: C:H.53, C:N.80, C:Y.106, D:S.48, D:A.49, D:N.80 GOL.10: 8 residues within 4Å: Chain C: S.48, A.49, G.78, V.103, Y.106 Chain D: N.80, Y.107 Ligands: GOL.9 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:N.80, C:S.48, C:S.48, C:G.78 Water bridges: D:Y.107, C:G.78 GOL.11: 8 residues within 4Å: Chain C: N.80, Y.107 Chain D: S.48, A.49, G.78, V.103, Y.106 Ligands: GOL.9 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:N.80, C:N.80, D:S.48 Water bridges: C:Y.107, D:S.48, D:G.78, D:G.78, D:V.103

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

PO4.6: 2 residues within 4Å: Chain B: R.21, K.25 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.21, B:R.21 Salt bridges: B:R.21 PO4.7: 3 residues within 4Å: Chain B: Y.116, K.120, R.150 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.116, B:Y.116, B:R.150 Water bridges: B:Y.116 Salt bridges: B:K.120 PO4.13: 2 residues within 4Å: Chain D: R.21, K.25 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.21, D:R.21 Salt bridges: D:R.21 PO4.14: 3 residues within 4Å: Chain D: Y.116, K.120, R.150 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Y.116, D:Y.116, D:Y.116, D:R.150 Salt bridges: D:K.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dobson, R.C.J. et al., Conserved main-chain peptide distortions: A proposed role for Ile203 in catalysis by dihydrodipicolinate synthase. Protein Sci. (2008)

Release Date

2008-09-23

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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