SMTL ID : 3ird.1

Structure of dihydrodipicolinate synthase from Clostridium botulinum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

homo-tetramer

Ligands

4 x MLT: D-MALATE(Non-covalent)

MLT.1: 9 residues within 4Å: Chain A: A.9, T.44, T.45, Y.133, R.138, K.161, V.205, F.244, N.248 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.205 Hydrogen bonds: A:T.44, A:T.44, A:T.44, A:T.45, A:Y.133, A:Y.133, A:R.138, A:N.248 Water bridges: A:K.161, A:K.161, A:K.161 Salt bridges: A:R.138, A:K.161 MLT.7: 9 residues within 4Å: Chain B: A.9, T.44, T.45, Y.133, R.138, K.161, V.205, F.244, N.248 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:V.205 Hydrogen bonds: B:T.44, B:T.44, B:T.44, B:T.45, B:Y.133, B:Y.133, B:R.138, B:N.248 Water bridges: B:K.161, B:K.161, B:K.161 Salt bridges: B:R.138, B:K.161 MLT.13: 9 residues within 4Å: Chain C: A.9, T.44, T.45, Y.133, R.138, K.161, V.205, F.244, N.248 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:V.205 Hydrogen bonds: C:T.44, C:T.44, C:T.44, C:T.45, C:T.45, C:Y.133, C:R.138, C:N.248 Water bridges: C:Y.133, C:Y.133, C:K.161 Salt bridges: C:R.138, C:K.161 MLT.19: 9 residues within 4Å: Chain D: A.9, T.44, T.45, Y.133, R.138, K.161, V.205, F.244, N.248 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:V.205 Hydrogen bonds: D:T.44, D:T.44, D:T.44, D:T.45, D:T.45, D:Y.133, D:R.138, D:N.248 Water bridges: D:Y.133, D:Y.133, D:K.161 Salt bridges: D:R.138, D:K.161

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

NA.2: 3 residues within 4Å: Chain A: C.152, D.154, I.157 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.157 NA.8: 3 residues within 4Å: Chain B: C.152, D.154, I.157 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.154 NA.14: 3 residues within 4Å: Chain C: C.152, D.154, I.157 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.157 NA.20: 3 residues within 4Å: Chain D: C.152, D.154, I.157 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.154

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

CL.3: 7 residues within 4Å: Chain A: G.165, N.166, I.167 Chain C: G.165, N.166, I.167 Ligands: CL.15 Ligand excluded by PLIP CL.4: 9 residues within 4Å: Chain A: Y.106, Y.107, R.138, T.139 Chain D: Y.106, Y.107, R.138, T.139 Ligands: CL.22 Ligand excluded by PLIP CL.9: 7 residues within 4Å: Chain B: G.165, N.166, I.167 Chain D: G.165, N.166, I.167 Ligands: CL.21 Ligand excluded by PLIP CL.10: 9 residues within 4Å: Chain B: Y.106, Y.107, R.138, T.139 Chain C: Y.106, Y.107, R.138, T.139 Ligands: CL.16 Ligand excluded by PLIP CL.15: 7 residues within 4Å: Chain A: G.165, N.166, I.167 Chain C: G.165, N.166, I.167 Ligands: CL.3 Ligand excluded by PLIP CL.16: 9 residues within 4Å: Chain B: Y.106, Y.107, R.138, T.139 Chain C: Y.106, Y.107, R.138, T.139 Ligands: CL.10 Ligand excluded by PLIP CL.21: 7 residues within 4Å: Chain B: G.165, N.166, I.167 Chain D: G.165, N.166, I.167 Ligands: CL.9 Ligand excluded by PLIP CL.22: 9 residues within 4Å: Chain A: Y.106, Y.107, R.138, T.139 Chain D: Y.106, Y.107, R.138, T.139 Ligands: CL.4 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: T.254, N.257, D.265, L.266 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.265, A:L.266 Water bridges: A:T.254, A:N.257 GOL.6: 3 residues within 4Å: Chain A: M.259, L.290, M.291 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.290 GOL.11: 4 residues within 4Å: Chain B: T.254, N.257, D.265, L.266 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.265, B:L.266 Water bridges: B:T.254, B:N.257 GOL.12: 3 residues within 4Å: Chain B: M.259, L.290, M.291 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.290 GOL.17: 4 residues within 4Å: Chain C: T.254, N.257, D.265, L.266 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.266 Water bridges: C:T.254, C:N.257 GOL.18: 3 residues within 4Å: Chain C: M.259, L.290, M.291 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.290 GOL.23: 4 residues within 4Å: Chain D: T.254, N.257, D.265, L.266 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.266 Water bridges: D:T.254, D:N.257 GOL.24: 3 residues within 4Å: Chain D: M.259, L.290, M.291 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.290

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Atkinson, S. et al., Structure of Cbot-DHDPS. To be Published

Release Date

2009-09-22

Peptides

Dihydrodipicolinate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Dihydrodipicolinate synthase

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