SMTL ID : 7kg2.1 (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

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

EDO.1: 6 residues within 4Å: Chain A: D.250, E.251, Y.253, N.254, K.304, Y.305 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.253, A:N.254, A:K.304 EDO.2: 4 residues within 4Å: Chain A: P.152, G.156, C.157 Ligands: MG.11 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.158 EDO.3: 4 residues within 4Å: Chain A: S.212, G.214, E.240, Y.242 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.240 EDO.4: 4 residues within 4Å: Chain A: K.44, I.47, E.48, T.81 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.48, A:E.48, A:T.81 EDO.5: 2 residues within 4Å: Chain A: H.99 Chain B: R.284 No protein-ligand interaction detected (PLIP) EDO.6: 3 residues within 4Å: Chain A: I.19, M.198, K.216 No protein-ligand interaction detected (PLIP) EDO.7: 1 residues within 4Å: Chain A: E.36 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.36 EDO.18: 2 residues within 4Å: Chain A: R.284 Chain B: H.99 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.284 EDO.19: 6 residues within 4Å: Chain B: I.17, I.18, I.19, D.52, A.53, K.88 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.19, B:D.52 EDO.20: 1 residues within 4Å: Chain B: K.83 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.83 EDO.21: 5 residues within 4Å: Chain B: N.16, I.17, I.18, K.88, P.145 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.16, B:K.88 Water bridges: B:I.17, B:D.114 EDO.22: 5 residues within 4Å: Chain B: T.161, N.183, D.185, K.186, D.189 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.161, B:N.183, B:D.185 Water bridges: B:T.161 EDO.23: 6 residues within 4Å: Chain B: C.82, T.85, K.86, V.87, K.88, D.114 4 PLIP interactions: 4 interactions with chain B Water bridges: B:T.85, B:T.85, B:D.114, B:D.114

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

MG.8: 1 residues within 4Å: Chain A: T.85 No protein-ligand interaction detected (PLIP) MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.10: 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.3 MG.11: 5 residues within 4Å: Chain A: P.152, G.156 Chain B: P.152, G.153 Ligands: EDO.2 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain A: D.170 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.170, H2O.3 MG.24: 3 residues within 4Å: Chain B: S.212, G.214, Y.242 No protein-ligand interaction detected (PLIP)

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

ACT.13: 6 residues within 4Å: Chain A: V.151, R.154, K.178, G.202, F.260, N.264 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.264 Salt bridges: A:R.154 ACT.14: 4 residues within 4Å: Chain A: T.161, D.162, D.189, H.193 No protein-ligand interaction detected (PLIP) ACT.15: 6 residues within 4Å: Chain A: L.211, G.214, G.215, K.216, A.237, Y.242 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.242 Salt bridges: A:K.216 ACT.25: 6 residues within 4Å: Chain B: Y.149, 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

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

PGE.16: 6 residues within 4Å: Chain A: Q.128, Q.129, Y.132, D.162, T.163, K.166 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.166 PGE.26: 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

2 x HIS: HISTIDINE(Non-covalent)

HIS.17: 8 residues within 4Å: Chain A: S.63, A.64, L.66, K.71, Y.122 Chain B: N.96, E.100 Ligands: HIS.27 9 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B, 3 Ligand-Ligand interactions Hydrogen bonds: A:S.63, A:K.71, B:N.96, B:E.100, H.27 Water bridges: A:Y.122, A:Y.122 Hydrophobic interactions: H.27 Salt bridges: H.17 HIS.27: 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 11 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B, 4 Ligand-Ligand interactions Hydrogen bonds: A:N.96, A:N.96, B:S.63, B:A.64, B:K.71, B:Y.122, H.17, H.27 Water bridges: A:E.100 Hydrophobic interactions: H.17 Salt bridges: H.27

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
A

B
C

4-hydroxy-tetrahydrodipicolinate synthase

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