SMTL ID : 7kxg.1 (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

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

MG.1: 4 residues within 4Å: Chain A: N.183, I.184, D.185 Chain B: G.182 No protein-ligand interaction detected (PLIP) MG.2: 5 residues within 4Å: Chain A: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain B: D.239 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.239, B:D.239, H2O.6, H2O.9 MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Chain B: D.114 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain B: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.20: 4 residues within 4Å: Chain C: R.154, F.260, S.263, N.264 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain C: K.15, F.168, R.196 No protein-ligand interaction detected (PLIP) MG.22: 4 residues within 4Å: Chain C: E.240, N.241, Y.242, K.243 No protein-ligand interaction detected (PLIP) MG.28: 5 residues within 4Å: Chain D: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.29: 3 residues within 4Å: Chain D: R.154, F.260, N.264 No protein-ligand interaction detected (PLIP) MG.30: 5 residues within 4Å: Chain B: K.125 Chain D: R.154, F.260, S.263, N.264 No protein-ligand interaction detected (PLIP) MG.31: 2 residues within 4Å: Chain D: Q.140, V.142 No protein-ligand interaction detected (PLIP)

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

PGE.3: 5 residues within 4Å: Chain A: Q.129, Y.132, D.162, T.163, K.166 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.166 Water bridges: A:S.160 PGE.13: 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 PGE.23: 6 residues within 4Å: Chain C: Q.128, Q.129, Y.132, D.162, T.163, K.166 2 PLIP interactions: 2 interactions with chain C Water bridges: C:Q.129, C:D.170 PGE.32: 7 residues within 4Å: Chain D: Q.128, Q.129, Y.132, D.162, T.163, K.166 Ligands: EDO.36 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.166

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

PEG.4: 5 residues within 4Å: Chain A: H.68, H.71, L.104, F.107 Ligands: HIS.8 No protein-ligand interaction detected (PLIP) PEG.14: 4 residues within 4Å: Chain B: H.68, H.71, L.104, F.107 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.71 PEG.24: 3 residues within 4Å: Chain A: H.99 Chain C: T.67, R.284 2 PLIP interactions: 2 interactions with chain C Water bridges: C:G.32, C:R.284 PEG.33: 7 residues within 4Å: Chain D: L.66, T.67, H.68, H.71, L.104, F.107 Ligands: HIS.37 No protein-ligand interaction detected (PLIP)

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

EDO.5: 5 residues within 4Å: Chain A: Y.149, V.151, R.154, F.260, N.264 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Water bridges: C:K.125, C:K.125 Hydrogen bonds: A:R.154, A:N.264 EDO.6: 5 residues within 4Å: Chain A: G.182, E.203, A.205, I.206 Chain B: D.185 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:G.182, A:A.205 Hydrogen bonds: B:D.185 EDO.7: 7 residues within 4Å: Chain A: E.262, C.288, S.289, P.290, S.291 Chain C: T.127, Q.129 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:S.291 Water bridges: C:T.127, C:Q.128 EDO.16: 3 residues within 4Å: Chain B: P.152, G.156, C.157 No protein-ligand interaction detected (PLIP) EDO.17: 3 residues within 4Å: Chain B: H.99 Chain D: T.67, R.284 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.284 EDO.18: 8 residues within 4Å: Chain A: A.192, H.193 Chain B: D.250, E.251, Y.253, N.254, K.304, Y.305 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.253, B:N.254, B:N.254, B:K.304, B:Y.305 EDO.25: 4 residues within 4Å: Chain C: H.68, H.71, L.104, F.107 1 PLIP interactions: 1 interactions with chain C Water bridges: C:L.104 EDO.26: 3 residues within 4Å: Chain C: K.44, E.48, T.81 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.48, C:T.81 EDO.35: 3 residues within 4Å: Chain B: T.67, R.284 Chain D: H.99 No protein-ligand interaction detected (PLIP) EDO.36: 4 residues within 4Å: Chain D: T.127, Q.128, Q.129 Ligands: PGE.32 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.127, D:T.127, D:Q.129, D:Q.129 Water bridges: D:Q.128

4 x HIS: HISTIDINE(Non-covalent)

HIS.8: 8 residues within 4Å: Chain A: S.63, A.64, L.66, Y.122 Chain C: N.96, E.100 Ligands: PEG.4, HIS.27 5 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions, 2 interactions with chain C Hydrogen bonds: A:S.63, A:Y.122, C:N.96, C:N.96 Salt bridges: H.8 HIS.19: 7 residues within 4Å: Chain B: S.63, A.64, L.66, Y.122 Chain D: N.96, E.100 Ligands: HIS.37 7 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: D:N.96, D:E.100, B:A.64, B:Y.122, H.19 Water bridges: D:E.100 Salt bridges: H.19 HIS.27: 7 residues within 4Å: Chain A: N.96, E.100 Chain C: S.63, A.64, L.66, Y.122 Ligands: HIS.8 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: A:N.96, A:E.100, C:S.63, C:A.64, H.27 Salt bridges: H.27 HIS.37: 8 residues within 4Å: Chain B: N.96, E.100 Chain D: S.63, A.64, L.66, Y.122 Ligands: HIS.19, PEG.33 8 PLIP interactions: 3 interactions with chain B, 4 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: B:N.96, B:N.96, D:S.63 Water bridges: B:E.100, D:S.95, D:E.100, D:Y.122 Salt bridges: H.37

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

ACT.15: 4 residues within 4Å: Chain B: V.34, D.35, E.36, Q.37 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.37 Hydrogen bonds: B:D.35, B:E.36 ACT.34: 3 residues within 4Å: Chain D: K.15, F.168, R.196 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.196

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
A

B
B

C
C

D
D

4-hydroxy-tetrahydrodipicolinate synthase

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