SMTL ID : 7kg2.3 (2 other biounits)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59K mutant with pyruvate bound in the active site and L-histidine bound at the allosteric site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: L.274, E.299, K.303 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.299, A:K.303 EDO.2: 3 residues within 4Å: Chain A: Y.242, K.243, K.246 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.208 EDO.3: 5 residues within 4Å: Chain A: R.41, K.44, R.45, E.48, F.310 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.48, A:F.310 EDO.4: 5 residues within 4Å: Chain A: D.250, E.251, Y.253, N.254, Y.305 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.250, A:Y.253, A:N.254, A:Y.305 EDO.5: 2 residues within 4Å: Chain A: I.19, K.216 No protein-ligand interaction detected (PLIP) EDO.6: 2 residues within 4Å: Chain A: Y.273, L.274 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.276 EDO.7: 5 residues within 4Å: Chain A: Q.37, S.38, R.41, E.279 Ligands: PGE.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.41, A:R.41, A:E.279 EDO.18: 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:Q.140, B:E.172 Water bridges: B:A.139 EDO.19: 3 residues within 4Å: Chain B: F.283, R.284, L.285 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.285 Water bridges: B:L.285 EDO.20: 7 residues within 4Å: Chain B: L.211, G.214, G.215, K.216, A.237, L.238, Y.242 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.215, B:K.216 EDO.21: 2 residues within 4Å: Chain B: P.152, G.156 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.152 Water bridges: B:E.158

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

MG.8: 1 residues within 4Å: Chain A: E.48 No protein-ligand interaction detected (PLIP) MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

ACT.10: 7 residues within 4Å: Chain A: Y.149, V.151, 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.11: 6 residues within 4Å: Chain A: S.63, A.64, K.71, Y.122 Chain B: Y.123 Ligands: HIS.17 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:Y.122, A:Y.122 Salt bridges: A:K.71 Hydrophobic interactions: B:Y.123 ACT.23: 5 residues within 4Å: Chain B: V.151, R.154, K.178, G.202, N.264 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.264 Salt bridges: B:R.154 ACT.24: 4 residues within 4Å: Chain B: D.162, I.165, K.166, R.169 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:D.162 Hydrogen bonds: B:D.162 Water bridges: B:R.169 Salt bridges: B:R.169 ACT.25: 2 residues within 4Å: Chain B: K.44, E.48 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.44 Salt bridges: B:K.44

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

PGE.12: 5 residues within 4Å: Chain A: Q.129, Y.132, D.162, T.163, K.166 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.166 PGE.13: 2 residues within 4Å: Chain A: K.304, K.306 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.306 PGE.14: 4 residues within 4Å: Chain A: G.276, I.278, E.279 Ligands: EDO.7 No protein-ligand interaction detected (PLIP)

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

PEG.15: 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 PEG.16: 4 residues within 4Å: Chain A: T.161, D.162, D.189, H.193 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.162

2 x HIS: HISTIDINE(Non-covalent)

HIS.17: 10 residues within 4Å: Chain A: S.63, A.64, L.66, K.71, Y.122 Chain B: S.95, N.96, E.100 Ligands: ACT.11, HIS.26 8 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A, 3 Ligand-Ligand interactions Hydrogen bonds: B:N.96, B:N.96, A:K.71, A:K.71, H.26 Water bridges: A:Y.122 Hydrophobic interactions: H.26 Salt bridges: H.17 HIS.26: 8 residues within 4Å: Chain A: N.96, E.100 Chain B: S.63, A.64, L.66, K.71, Y.122 Ligands: HIS.17 8 PLIP interactions: 3 interactions with chain B, 3 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: B:S.63, B:K.71, B:Y.122, H.17, A:N.96, A:N.96 Hydrophobic interactions: H.17 Salt bridges: H.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Majdi Yazdi, M.M. et al., Reversing the roles of a crucial hydrogen-bonding pair: a lysine-insensitive mutant of Campylobacter jejuni dihydrodipicolinate synthase, H59K, binds histidine in its allosteric site. 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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