SMTL ID : 7kg9.3 (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

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

EDO.1: 8 residues within 4Å: Chain A: E.179, A.180, S.181, G.182, N.183, C.187, E.203, I.206 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.179, A:E.179, A:S.181, A:G.182, A:N.183, A:N.183, A:E.203 EDO.2: 9 residues within 4Å: Chain A: K.178, G.202, E.203, D.204, I.219, S.220, V.221, F.260 Ligands: EDO.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.204, A:D.204, A:I.219, A:V.221 EDO.3: 7 residues within 4Å: Chain A: E.203, D.204, A.205, N.256, K.257, F.260 Ligands: EDO.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.203, A:D.204, A:A.205 EDO.9: 5 residues within 4Å: Chain B: K.15, F.168, R.169, D.170, E.172 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.170 EDO.10: 4 residues within 4Å: Chain B: D.250, E.251, Y.253, N.254 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.253, B:N.254 EDO.11: 1 residues within 4Å: Chain B: D.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.14

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

MG.4: 4 residues within 4Å: Chain A: G.94, L.117, S.118, V.119 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.117 MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain B: D.162, D.189 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.162, H2O.9, H2O.9, H2O.10 MG.15: 3 residues within 4Å: Chain B: S.231, A.232, H.235 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.235, H2O.8

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

PEG.6: 3 residues within 4Å: Chain A: E.48, T.81, T.85 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.81 PEG.16: 5 residues within 4Å: Chain B: R.72, G.103, K.106, F.107, E.110 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.110 PEG.17: 5 residues within 4Å: Chain B: K.136, Q.140, D.170, C.171, E.172 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.132, B:Q.140, B:E.172

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

PG4.7: 5 residues within 4Å: Chain A: 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

2 x LYS: LYSINE(Non-covalent)

LYS.8: 10 residues within 4Å: Chain A: S.63, A.64, L.66, T.67, H.71, E.100, Y.122 Chain B: N.96, E.100 Ligands: LYS.18 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.63, A:H.71, A:N.96, B:N.96, B:E.100 LYS.18: 9 residues within 4Å: Chain A: N.96, E.100 Chain B: S.63, A.64, L.66, W.68, H.71, Y.122 Ligands: LYS.8 7 PLIP interactions: 1 Ligand-Ligand interactions, 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: K.18, B:A.64, B:H.71, B:Y.122, A:N.96, A:N.96 Hydrophobic interactions: B:W.68

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

PGE.12: 8 residues within 4Å: Chain A: K.125 Chain B: T.59, V.151, R.154, K.178, F.260, S.263, N.264 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.154, B:N.264, B:N.264, A:K.125 PGE.13: 3 residues within 4Å: Chain B: L.274, A.275, G.276 No protein-ligand interaction detected (PLIP)

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
D

B
F

4-hydroxy-tetrahydrodipicolinate synthase

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