SMTL ID : 7kg2.2 (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

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

EDO.1: 5 residues within 4Å: Chain A: S.212, G.214, E.240, Y.242 Ligands: EDO.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.240, A:Y.242 Water bridges: A:K.216 EDO.2: 3 residues within 4Å: Chain A: K.44, E.48, T.81 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.81 EDO.3: 4 residues within 4Å: Chain A: P.195, G.214, K.216 Ligands: EDO.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.214, A:K.216 EDO.4: 6 residues within 4Å: Chain A: F.283, R.284, L.285 Chain B: H.99 Ligands: EDO.19, MG.25 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.99, A:F.283, A:L.285 EDO.5: 7 residues within 4Å: Chain A: P.152, G.153, G.156 Chain B: P.152, G.153, G.156 Ligands: PEG.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.125, A:G.153 EDO.14: 5 residues within 4Å: Chain B: D.250, E.251, Y.253, N.254, Y.305 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.253, B:N.254 EDO.15: 5 residues within 4Å: Chain B: E.48, N.49, G.50, K.308 Ligands: EDO.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.231, B:S.231, B:K.308 EDO.16: 4 residues within 4Å: Chain B: E.48, N.49, K.308 Ligands: EDO.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.308 EDO.17: 4 residues within 4Å: Chain B: C.82, V.87, K.88, D.114 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:C.82 Water bridges: B:K.86, B:K.86 EDO.18: 5 residues within 4Å: Chain B: K.44, I.47, E.48, T.81, T.85 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.48, B:E.48, B:T.81 EDO.19: 4 residues within 4Å: Chain A: T.67, R.284 Chain B: H.99 Ligands: EDO.4 No protein-ligand interaction detected (PLIP) EDO.20: 8 residues within 4Å: Chain B: L.211, G.214, G.215, K.216, A.237, L.238, Y.242 Ligands: ACT.28 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.214, B:G.215, B:K.216, B:Y.242 EDO.21: 6 residues within 4Å: Chain B: F.29, G.32, E.282, F.283, R.284 Ligands: MG.24 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.32, B:E.282, B:E.282, B:R.284, B:R.284 EDO.22: 5 residues within 4Å: Chain B: E.36, T.73, E.76, I.77, E.80 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.36, B:E.80

5 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 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.2 MG.7: 1 residues within 4Å: Chain A: D.114 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.114, H2O.2 MG.23: 1 residues within 4Å: Chain B: D.52 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.52, H2O.9, H2O.9 MG.24: 3 residues within 4Å: Chain B: R.284, L.285 Ligands: EDO.21 No protein-ligand interaction detected (PLIP) MG.25: 5 residues within 4Å: Chain A: R.284, L.285 Chain B: T.98, H.99 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.285

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

ACT.8: 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.9: 4 residues within 4Å: Chain A: T.161, D.162, D.189, H.193 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.161, A:D.162 Salt bridges: A:H.193 ACT.10: 3 residues within 4Å: Chain A: H.99 Chain B: K.33, T.67 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.67 Salt bridges: B:K.33, B:R.284, A:H.99 ACT.26: 7 residues within 4Å: Chain B: Y.149, V.151, R.154, K.178, G.202, F.260, N.264 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.149, B:N.264 Salt bridges: B:R.154 ACT.27: 3 residues within 4Å: Chain B: D.162, D.189, H.193 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.162 Salt bridges: B:H.193 ACT.28: 4 residues within 4Å: Chain B: S.212, G.214, Y.242 Ligands: EDO.20 No protein-ligand interaction detected (PLIP)

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

PGE.11: 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.12: 3 residues within 4Å: Chain A: K.303, K.304, K.306 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.306 PGE.29: 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.13: 9 residues within 4Å: Chain A: S.63, A.64, L.66, K.71, Y.122 Chain B: S.95, N.96, E.100 Ligands: HIS.34 10 PLIP interactions: 6 interactions with chain A, 2 Ligand-Ligand interactions, 2 interactions with chain B Hydrogen bonds: A:S.63, A:A.64, A:K.71, H.13, B:N.96, B:N.96 Water bridges: A:Y.122, A:Y.122, A:Y.122 Salt bridges: H.13 HIS.34: 8 residues within 4Å: Chain A: N.96, E.100 Chain B: S.63, A.64, L.66, K.71, Y.122 Ligands: HIS.13 6 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: B:K.71, B:K.71, B:Y.122, A:N.96, A:N.96 Salt bridges: H.34

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

PG4.30: 1 residues within 4Å: Chain B: K.86 No protein-ligand interaction detected (PLIP)

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

PEG.31: 3 residues within 4Å: Chain B: P.152, G.156 Ligands: EDO.5 No protein-ligand interaction detected (PLIP) PEG.32: 4 residues within 4Å: Chain B: I.19, M.198, K.216, L.238 No protein-ligand interaction detected (PLIP) PEG.33: 6 residues within 4Å: Chain B: A.275, G.276, L.277, I.307, G.309, F.310 1 PLIP interactions: 1 interactions with chain B Water bridges: B:F.310

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
B

B
D

4-hydroxy-tetrahydrodipicolinate synthase

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