SMTL ID : 7kg5.1 (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

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 1 residues within 4Å: Chain A: D.239 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.239, H2O.5 MG.2: 4 residues within 4Å: Chain A: V.34, D.35, E.36, Q.37 No protein-ligand interaction detected (PLIP) MG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain B: D.52 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.52, H2O.8, H2O.11, H2O.11

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

EDO.3: 8 residues within 4Å: Chain A: V.57, G.58, S.63, H.71, G.92, A.93, G.94, L.104 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.63, A:G.94 Water bridges: A:H.71, A:G.92, A:A.93, A:L.117 EDO.4: 5 residues within 4Å: Chain A: Y.149, V.151, R.154, F.260, N.264 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.154, A:N.264 EDO.5: 5 residues within 4Å: Chain A: T.161, N.183, D.185, K.186, D.189 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.161, A:D.189, A:D.189 EDO.6: 4 residues within 4Å: Chain A: T.65, L.66 Chain B: A.97, H.99 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.99 EDO.7: 4 residues within 4Å: Chain A: L.191, P.195, G.214, K.216 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.216 Water bridges: A:L.191 EDO.8: 4 residues within 4Å: Chain A: E.76, V.79, E.80, H.111 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.80 EDO.15: 6 residues within 4Å: Chain A: K.125 Chain B: R.154, F.260, S.263, N.264 Ligands: ACT.19 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.154, B:N.264, A:K.125 EDO.16: 7 residues within 4Å: Chain B: L.211, G.214, G.215, K.216, A.237, L.238, Y.242 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.215, B:K.216, B:Y.242

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

PEG.9: 5 residues within 4Å: Chain A: W.68, H.99, E.100, G.103, L.104 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.99, A:G.103 PEG.10: 8 residues within 4Å: Chain A: L.25, I.26, Y.39, L.42, R.45, Q.46, N.224, M.272 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.26, A:L.42, A:R.45, A:Q.46 PEG.17: 5 residues within 4Å: Chain B: K.44, I.47, E.48, T.81, T.85 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.48 PEG.18: 5 residues within 4Å: Chain B: H.99, E.100, G.103, L.104, F.107 No protein-ligand interaction detected (PLIP)

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

ACT.11: 3 residues within 4Å: Chain A: S.212, E.240, Y.242 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.242 Hydrogen bonds: A:S.212, A:Y.242 ACT.19: 5 residues within 4Å: Chain B: Y.149, R.154, K.178, N.264 Ligands: EDO.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.149, B:N.264 Salt bridges: B:R.154 ACT.20: 5 residues within 4Å: Chain B: I.19, G.20, D.52, H.235, L.238 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.52

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.12: 6 residues within 4Å: Chain A: Q.128, Q.129, Y.132, D.162, T.163, K.166 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.162, A:K.166 PG4.21: 6 residues within 4Å: Chain B: Q.128, Q.129, Y.132, D.162, T.163, K.166 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.166 Water bridges: B:Q.129

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
D

4-hydroxy-tetrahydrodipicolinate synthase

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