SMTL ID : 7kg9.1 (2 other biounits)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H56W mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: V.57, S.63, H.71, G.92, A.93, G.94 Ligands: LYS.7 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:S.63, A:G.92, A:G.94, K.7 Water bridges: A:A.93, A:Y.122 EDO.2: 3 residues within 4Å: Chain A: T.67, E.69, E.70 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.67, A:E.70 Water bridges: A:T.73 EDO.3: 5 residues within 4Å: Chain A: A.180, S.181, G.182, E.203 Ligands: GOL.6 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.181

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

PGE.4: 4 residues within 4Å: Chain A: Q.129, D.162, T.163, K.166 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.166

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

PEG.5: 5 residues within 4Å: Chain A: W.68, E.100 Chain B: W.68, E.100 Ligands: LYS.9 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:E.100 Water bridges: K.9

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: T.59, Y.149, V.151, R.154, K.178, A.180, N.264 Ligands: EDO.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.149, A:Y.149, A:N.264

2 x LYS: LYSINE(Non-covalent)

LYS.7: 11 residues within 4Å: Chain A: S.63, A.64, L.66, W.68, H.71, Y.122 Chain B: S.95, N.96, E.100 Ligands: EDO.1, LYS.9 9 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: B:N.96, B:E.100, A:A.64, A:H.71, K.9 Water bridges: B:Y.122, A:Y.122, A:Y.122 Salt bridges: K.7 LYS.9: 10 residues within 4Å: Chain A: N.96, E.100 Chain B: S.63, A.64, L.66, W.68, H.71, Y.122 Ligands: PEG.5, LYS.7 7 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: B:W.68 Hydrogen bonds: B:H.71, B:Y.122, A:N.96, A:N.96, K.7, K.7

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

ACT.8: 2 residues within 4Å: Chain A: A.192, H.193 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.193

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
A

B
E

4-hydroxy-tetrahydrodipicolinate synthase

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