SMTL ID : 7kn9.1 (2 other biounits)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, E88A mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

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

MG.1: 1 residues within 4Å: Chain A: D.239 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.239, H2O.3, H2O.5 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.3: 2 residues within 4Å: Chain A: E.69, E.70 No protein-ligand interaction detected (PLIP) MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain A: Y.273 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain A: S.95, Y.122 Ligands: ACT.14, LYS.17 3 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:S.95, H2O.5, ACT.14 MG.18: 1 residues within 4Å: Chain B: D.52 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.52, H2O.10, H2O.13, H2O.14 MG.19: 2 residues within 4Å: Chain B: S.291, K.292 No protein-ligand interaction detected (PLIP) MG.20: 5 residues within 4Å: Chain B: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain B: S.291, E.293, N.294 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.291, H2O.15 MG.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

PGE.7: 6 residues within 4Å: Chain A: Q.128, 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:D.170 PGE.8: 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.23: 5 residues within 4Å: Chain B: Q.128, Q.129, D.162, T.163, K.166 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.166 Water bridges: B:Q.129

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

EDO.9: 3 residues within 4Å: Chain A: P.152, G.156, C.157 No protein-ligand interaction detected (PLIP) EDO.10: 9 residues within 4Å: Chain A: L.211, G.214, G.215, K.216, A.237, L.238, E.240, Y.242 Ligands: EDO.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.215, A:K.216 EDO.11: 1 residues within 4Å: Chain A: D.114 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.114 EDO.12: 5 residues within 4Å: Chain A: S.212, G.214, E.240, Y.242 Ligands: EDO.10 No protein-ligand interaction detected (PLIP) EDO.13: 4 residues within 4Å: Chain A: L.191, P.195, G.214, K.216 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.216 EDO.24: 3 residues within 4Å: Chain B: S.212, G.214, Y.242 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.242 EDO.25: 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 EDO.26: 5 residues within 4Å: Chain B: D.250, E.251, Y.253, N.254, Y.305 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.253, B:N.254, B:Y.305 EDO.27: 8 residues within 4Å: Chain A: A.64 Chain B: H.68, S.95, A.97, H.99, A.100 Ligands: LYS.17, LYS.30 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: B:H.68, A:A.64, K.17

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

ACT.14: 7 residues within 4Å: Chain A: H.68, A.97, A.100 Chain B: A.64 Ligands: MG.6, LYS.17, LYS.30 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.97, A:A.100 Water bridges: A:H.99 Salt bridges: A:H.68 ACT.15: 4 residues within 4Å: Chain A: T.67, E.70, R.284 Chain B: H.99 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.284, B:H.99 ACT.28: 4 residues within 4Å: Chain B: I.19, D.52, H.235, L.238 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.52 ACT.29: 4 residues within 4Å: Chain B: A.275, I.307, K.308, G.309 No protein-ligand interaction detected (PLIP)

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

PEG.16: 6 residues within 4Å: Chain A: E.203, D.204, A.205, N.256, K.257, F.260 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.203, A:A.205 Water bridges: A:D.204, A:K.257, A:K.257

2 x LYS: LYSINE(Non-covalent)

LYS.17: 12 residues within 4Å: Chain A: S.63, A.64, L.66, H.68, H.71, N.96, Y.122 Chain B: N.96 Ligands: MG.6, ACT.14, EDO.27, LYS.30 7 PLIP interactions: 2 interactions with chain A, 3 Ligand-Ligand interactions, 2 interactions with chain B Hydrogen bonds: A:H.71, A:Y.122, K.30, K.30, B:N.96, B:N.96 Salt bridges: K.17 LYS.30: 11 residues within 4Å: Chain A: N.96 Chain B: S.63, A.64, L.66, H.68, H.71, N.96, Y.122 Ligands: ACT.14, LYS.17, EDO.27 8 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 4 Ligand-Ligand interactions Hydrogen bonds: A:N.96, A:N.96, B:A.64, B:H.71, K.17, K.30 Water bridges: K.17 Salt bridges: K.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saran, S. et al., THE ALLOSTERIC SITE RESIDUE, E88 INTERACTS WITH THE INHIBITORS TO TRANSMIT THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS BY FORMING A HYDROGEN BOND. To Be Published

Release Date

2021-11-17

Peptides

4-hydroxy-tetrahydrodipicolinate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

4-hydroxy-tetrahydrodipicolinate synthase

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