SMTL ID : 7kg5.2 (2 other biounits)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H56W mutant with pyruvate bound in the active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 6 residues within 4Å: Chain A: Q.128, Q.129, Y.132, D.162, T.163, K.166 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.162, A:D.162, A:K.166 PGE.2: 5 residues within 4Å: Chain A: K.44, I.47, E.48, G.50 Ligands: EDO.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.44, A:G.50 PGE.14: 5 residues within 4Å: Chain B: Q.129, Y.132, D.162, T.163, K.166 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.166

5 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 1 residues within 4Å: Chain A: D.239 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.239, H2O.3, H2O.5 MG.4: 1 residues within 4Å: Chain A: T.85 No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain A: R.154, F.260, S.263, N.264 Ligands: EDO.6 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain B: W.68, E.100 No protein-ligand interaction detected (PLIP) MG.16: 6 residues within 4Å: Chain B: S.63, A.64, L.66, W.68, H.71 Ligands: PEG.22 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.63

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 5 residues within 4Å: Chain A: V.151, R.154, F.260, N.264 Ligands: MG.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.154, A:N.264 EDO.7: 3 residues within 4Å: Chain A: G.50, K.86 Ligands: PGE.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.86, A:K.86 Water bridges: A:N.49 EDO.8: 3 residues within 4Å: Chain A: P.152, G.156, C.157 2 PLIP interactions: 2 interactions with chain A Water bridges: A:P.152, A:E.158 EDO.9: 8 residues within 4Å: Chain A: L.211, G.214, G.215, K.216, A.237, L.238, Y.242 Ligands: EDO.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.211, A:K.216, A:Y.242 EDO.10: 6 residues within 4Å: Chain A: D.250, E.251, Y.253, N.254, K.304, Y.305 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.253, A:N.254, A:K.304 EDO.11: 5 residues within 4Å: Chain A: S.212, G.214, E.240, Y.242 Ligands: EDO.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.212, A:E.240, A:E.240 EDO.12: 4 residues within 4Å: Chain A: D.162, I.165, K.166 Ligands: GOL.13 No protein-ligand interaction detected (PLIP) EDO.17: 5 residues within 4Å: Chain B: I.17, I.18, I.19, D.52, K.88 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.19, B:D.52 Water bridges: B:I.17 EDO.18: 3 residues within 4Å: Chain B: K.15, F.168, R.196 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.15 EDO.19: 5 residues within 4Å: Chain B: D.250, E.251, Y.253, N.254, Y.305 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.253, B:N.254, B:Y.305 EDO.20: 2 residues within 4Å: Chain B: G.103, F.107 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.99 EDO.21: 5 residues within 4Å: Chain B: K.15, F.168, R.169, C.171, E.172 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.15, B:K.15, B:E.172

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 3 residues within 4Å: Chain A: D.162, D.189 Ligands: EDO.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.189 Water bridges: A:D.162 GOL.27: 4 residues within 4Å: Chain B: T.161, D.162, D.189, H.193 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.162 Water bridges: B:D.162, B:D.162

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.22: 8 residues within 4Å: Chain A: N.96, Y.123 Chain B: S.63, A.64, W.68, G.94, Y.122 Ligands: MG.16 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.96, A:N.96, B:S.63 Water bridges: B:Y.122 PEG.23: 7 residues within 4Å: Chain A: A.64, T.65, L.66, T.67 Chain B: A.97, H.99, E.100 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:H.99, B:E.100 Water bridges: B:T.98, A:A.64, A:W.68, A:H.71 PEG.24: 5 residues within 4Å: Chain B: I.47, E.48, N.49, G.50, K.86 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.86, B:K.86

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.25: 5 residues within 4Å: Chain B: R.154, K.178, G.202, F.260, N.264 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.260 Hydrogen bonds: B:N.264 Salt bridges: B:R.154 ACT.26: 3 residues within 4Å: Chain B: S.212, G.214, Y.242 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Majdi Yazd, M. et al., Fluorescence-based Assay Development for Screening Novel Inhibitors of Dihydrodipicolinate Synthase from Campylobacter jejuni. To Be Published

Release Date

2021-10-20

Peptides

4-hydroxy-tetrahydrodipicolinate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

4-hydroxy-tetrahydrodipicolinate synthase

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