SMTL ID : 7kh4.1 (2 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

1 x 3VN: (2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid(Non-covalent)

3VN.1: 17 residues within 4Å: Chain A: S.63, A.64, L.66, W.68, H.71, N.96, E.100, Y.122 Chain B: S.63, A.64, L.66, W.68, H.71, N.96, E.100, Y.122 Ligands: PEG.17 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:W.68, A:W.68 Hydrogen bonds: B:H.71, B:N.96, B:N.96, B:N.96, A:H.71, A:N.96, A:N.96, A:E.100, A:Y.122 Water bridges: B:Y.122

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

MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 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.4 MG.5: 1 residues within 4Å: Chain A: E.36 No protein-ligand interaction detected (PLIP) MG.21: 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.13 MG.22: 5 residues within 4Å: Chain B: R.154, F.260, S.263, N.264 Ligands: EDO.26 No protein-ligand interaction detected (PLIP) MG.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.24: 2 residues within 4Å: Chain B: E.300, K.303 No protein-ligand interaction detected (PLIP)

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

PG4.6: 7 residues within 4Å: Chain A: Q.128, Q.129, Y.132, D.162, T.163, K.166 Ligands: EDO.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.166 Water bridges: A:Q.129, A:Q.129 PG4.25: 6 residues within 4Å: Chain B: Q.128, Q.129, Y.132, D.162, T.163, K.166 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.166

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

EDO.7: 3 residues within 4Å: Chain A: I.47, E.48, G.50 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.50 EDO.8: 3 residues within 4Å: Chain A: T.127, Q.128 Chain B: E.262 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.128, B:E.262 Water bridges: A:Q.129, B:S.263, B:N.294 EDO.9: 5 residues within 4Å: Chain A: W.68, R.72, G.103, L.104, F.107 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.72, A:R.72 EDO.10: 2 residues within 4Å: Chain A: H.99 Chain B: R.284 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.284 EDO.11: 4 residues within 4Å: Chain A: Q.37, A.40, R.41, K.44 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.44 EDO.12: 3 residues within 4Å: Chain A: K.166, D.170 Ligands: PG4.6 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.169 EDO.13: 4 residues within 4Å: Chain A: S.212, G.214, Y.242 Ligands: EDO.14 No protein-ligand interaction detected (PLIP) EDO.14: 9 residues within 4Å: Chain A: L.211, G.214, G.215, K.216, A.237, L.238, E.240, Y.242 Ligands: EDO.13 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.215, A:K.216, A:E.240, A:E.240, A:Y.242 EDO.15: 4 residues within 4Å: Chain A: A.180, S.181, G.182, E.203 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.182 EDO.16: 2 residues within 4Å: Chain A: I.19, K.216 No protein-ligand interaction detected (PLIP) EDO.26: 5 residues within 4Å: Chain B: T.59, R.154, F.260, N.264 Ligands: MG.22 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.264 Water bridges: B:R.154, B:R.154 EDO.27: 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

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

PEG.17: 5 residues within 4Å: Chain A: W.68, E.100 Chain B: W.68, E.100 Ligands: 3VN.1 No protein-ligand interaction detected (PLIP) PEG.18: 4 residues within 4Å: Chain A: K.125, P.152, G.153, G.156 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.125, A:K.125 PEG.28: 6 residues within 4Å: Chain B: W.68, R.72, H.99, G.103, L.104, F.107 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.72 PEG.29: 2 residues within 4Å: Chain A: R.284 Chain B: H.99 No protein-ligand interaction detected (PLIP)

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

ACT.19: 3 residues within 4Å: Chain A: Y.273, G.276, I.278 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.273 Hydrogen bonds: A:Y.273 ACT.20: 3 residues within 4Å: Chain A: D.228, A.232, I.248 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.248 Hydrogen bonds: A:D.228 ACT.30: 4 residues within 4Å: Chain B: I.19, D.52, H.235, L.238 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.19, B:L.238 Salt bridges: B:H.235 ACT.31: 4 residues within 4Å: Chain B: K.44, I.47, E.48, T.85 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.48 ACT.32: 2 residues within 4Å: Chain B: F.168, R.196 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.15, B:R.196 ACT.33: 3 residues within 4Å: Chain B: I.17, I.19, M.198 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.19

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

2021-10-27

Peptides

4-hydroxy-tetrahydrodipicolinate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
F

4-hydroxy-tetrahydrodipicolinate synthase

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