SMTL ID : 7kxg.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: Q.37, S.38, R.41 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain B: R.154, F.260, N.264 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain B: R.154, F.260, S.263, N.264 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain A: T.67 Chain B: H.99 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain C: Q.37, S.38, R.41 No protein-ligand interaction detected (PLIP) MG.26: 3 residues within 4Å: Chain D: R.154, F.260, N.264 No protein-ligand interaction detected (PLIP) MG.27: 4 residues within 4Å: Chain D: R.154, F.260, S.263, N.264 No protein-ligand interaction detected (PLIP) MG.28: 2 residues within 4Å: Chain C: T.67 Chain D: H.99 No protein-ligand interaction detected (PLIP)

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

PGE.2: 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:Y.132 PGE.3: 6 residues within 4Å: Chain A: T.67, H.68, H.71, L.104, F.107 Ligands: HIS.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.68 Water bridges: A:H.68 PGE.11: 7 residues within 4Å: Chain B: L.66, T.67, H.68, H.71, L.104, F.107 Ligands: HIS.17 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.68 PGE.20: 5 residues within 4Å: Chain C: Q.129, Y.132, D.162, T.163, K.166 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.132 Water bridges: C:Y.132 PGE.21: 6 residues within 4Å: Chain C: T.67, H.68, H.71, L.104, F.107 Ligands: HIS.25 1 PLIP interactions: 1 interactions with chain C Water bridges: C:H.68 PGE.29: 7 residues within 4Å: Chain D: L.66, T.67, H.68, H.71, L.104, F.107 Ligands: HIS.35 1 PLIP interactions: 1 interactions with chain D Water bridges: D:H.68

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

ACT.4: 7 residues within 4Å: Chain A: Y.149, V.151, R.154, K.178, G.202, F.260, N.264 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.260 Hydrogen bonds: A:N.264 Salt bridges: A:R.154 ACT.5: 5 residues within 4Å: Chain A: S.63, A.64, Y.122 Chain B: Y.123 Ligands: HIS.7 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.63 Hydrophobic interactions: B:Y.123 ACT.13: 4 residues within 4Å: Chain B: K.15, F.168, R.169, E.172 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.169 Salt bridges: B:K.15 ACT.22: 7 residues within 4Å: Chain C: Y.149, V.151, R.154, K.178, G.202, F.260, N.264 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.260 Hydrogen bonds: C:N.264 Salt bridges: C:R.154 ACT.23: 5 residues within 4Å: Chain C: S.63, A.64, Y.122 Chain D: Y.123 Ligands: HIS.25 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.123 Hydrogen bonds: C:S.63, C:Y.122 ACT.31: 4 residues within 4Å: Chain D: K.15, F.168, R.169, E.172 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.169 Salt bridges: D:K.15

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

EDO.6: 6 residues within 4Å: Chain A: E.203, D.204, A.205, N.256, K.257, F.260 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.205, A:K.257 Water bridges: A:G.202, A:D.204 EDO.14: 2 residues within 4Å: Chain B: Y.273, L.274 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.273 EDO.15: 4 residues within 4Å: Chain B: F.283, R.284, L.285 Ligands: EDO.16 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:H.99 Hydrogen bonds: B:F.283, B:L.285 EDO.16: 4 residues within 4Å: Chain A: H.99 Chain B: T.67, R.284 Ligands: EDO.15 No protein-ligand interaction detected (PLIP) EDO.24: 6 residues within 4Å: Chain C: E.203, D.204, A.205, N.256, K.257, F.260 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.205, C:K.257 Water bridges: C:G.202, C:D.204 EDO.32: 2 residues within 4Å: Chain D: Y.273, L.274 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.273 EDO.33: 4 residues within 4Å: Chain D: F.283, R.284, L.285 Ligands: EDO.34 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:F.283, D:L.285 Water bridges: C:H.99 EDO.34: 4 residues within 4Å: Chain C: H.99 Chain D: T.67, R.284 Ligands: EDO.33 No protein-ligand interaction detected (PLIP)

4 x HIS: HISTIDINE(Non-covalent)

HIS.7: 9 residues within 4Å: Chain A: S.63, A.64, L.66, Y.122 Chain B: N.96, E.100 Ligands: PGE.3, ACT.5, HIS.17 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: A:A.64, A:Y.122, B:N.96, B:E.100, H.7 Salt bridges: H.7 HIS.17: 8 residues within 4Å: Chain A: N.96, E.100 Chain B: S.63, A.64, L.66, Y.122 Ligands: HIS.7, PGE.11 7 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: A:N.96, A:E.100, B:S.63 Water bridges: B:S.95, B:E.100, B:Y.122 Salt bridges: H.17 HIS.25: 9 residues within 4Å: Chain C: S.63, A.64, L.66, Y.122 Chain D: N.96, E.100 Ligands: PGE.21, ACT.23, HIS.35 7 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: D:N.96, D:E.100, C:A.64, H.25 Water bridges: D:E.100, C:Y.122 Salt bridges: H.25 HIS.35: 8 residues within 4Å: Chain C: N.96, E.100 Chain D: S.63, A.64, L.66, Y.122 Ligands: HIS.25, PGE.29 8 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: C:N.96, C:E.100, D:S.63, D:Y.122 Water bridges: C:E.100, D:S.95, D:E.100 Salt bridges: H.35

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

PEG.12: 5 residues within 4Å: Chain B: Q.129, Y.132, D.162, T.163, K.166 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.163, B:K.166 Water bridges: B:Q.129, B:S.160 PEG.30: 5 residues within 4Å: Chain D: Q.129, Y.132, D.162, T.163, K.166 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.166 Water bridges: D:Q.129, D:S.160

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.18: 5 residues within 4Å: Chain B: K.136, Q.140, D.170, C.171, E.172 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.140, B:E.172 GOL.36: 5 residues within 4Å: Chain D: K.136, Q.140, D.170, C.171, E.172 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.140, D:E.172

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

2021-12-08

Peptides

4-hydroxy-tetrahydrodipicolinate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
E

D
F

4-hydroxy-tetrahydrodipicolinate synthase

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