SMTL ID : 7kg5.3 (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

1 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.166 Water bridges: A:Q.129

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.127, Q.128 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain A: C.288, S.289 Chain B: Q.129 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.289, H2O.8 MG.12: 4 residues within 4Å: Chain B: R.154, F.260, S.263, N.264 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain B: A.64, L.66 No protein-ligand interaction detected (PLIP)

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

EDO.4: 1 residues within 4Å: Chain A: F.310 1 PLIP interactions: 1 interactions with chain A Water bridges: A:F.310 EDO.5: 5 residues within 4Å: Chain A: E.133 Chain B: F.283, L.285, L.287, C.288 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.133, B:F.283 Water bridges: B:F.283 EDO.6: 4 residues within 4Å: Chain A: V.34, D.35, E.36, Q.37 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.34, A:E.36, A:Q.37 EDO.7: 4 residues within 4Å: Chain A: L.274, E.299, M.302, K.303 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.299, A:K.303 EDO.8: 7 residues within 4Å: Chain A: P.152, G.153, G.156 Chain B: K.125, P.152, G.153, G.156 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.125, B:K.125, B:G.153 EDO.14: 5 residues within 4Å: Chain B: Q.129, D.162, T.163, K.166 Ligands: EDO.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.166 Water bridges: B:S.160, B:S.160 EDO.15: 4 residues within 4Å: Chain B: T.127, Q.128, Q.129 Ligands: EDO.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.128, B:Q.129 Water bridges: B:T.127

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

ACT.9: 6 residues within 4Å: Chain A: Y.149, R.154, K.178, G.202, F.260, N.264 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.260 Hydrogen bonds: A:Y.149, A:N.264 Salt bridges: A:R.154 ACT.18: 2 residues within 4Å: Chain B: Y.273, L.274 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.274 ACT.19: 4 residues within 4Å: Chain B: Y.149, R.154, K.178, N.264 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.202, B:N.264 Salt bridges: B:R.154 ACT.20: 3 residues within 4Å: Chain B: H.235, F.236, D.239 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:H.235 Hydrogen bonds: B:D.239

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 4 residues within 4Å: Chain A: T.161, D.162, D.189, H.193 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.162 Water bridges: A:D.162 GOL.11: 2 residues within 4Å: Chain A: E.100 Chain B: E.100 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.64, B:E.100 Water bridges: A:A.64

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

PEG.16: 6 residues within 4Å: Chain B: K.136, Q.140, D.170, C.171, E.172 Ligands: PEG.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.140, B:E.172 PEG.17: 6 residues within 4Å: Chain B: A.139, Q.140, V.142, D.143, N.173 Ligands: PEG.16 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.173, B:N.173

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
E

B
F

4-hydroxy-tetrahydrodipicolinate synthase

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