SMTL ID : 7kwp.1 (1 other biounit)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni with pyruvate bound in the active site and L-lysine bound at the allosteric site in C2221 space group

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

homo-tetramer

Ligands

4 x LYS: LYSINE(Non-covalent)

LYS.1: 11 residues within 4Å: Chain A: S.63, A.64, L.66, H.68, H.71, N.96, Y.122 Chain D: N.96, A.97, E.100 Ligands: LYS.13 6 PLIP interactions: 2 interactions with chain A, 2 Ligand-Ligand interactions, 2 interactions with chain D Hydrogen bonds: A:A.64, A:H.71, K.1, D:N.96, D:N.96 Salt bridges: K.1 LYS.4: 9 residues within 4Å: Chain B: S.63, A.64, L.66, H.68, H.71, Y.122 Chain C: N.96, E.100 Ligands: LYS.10 9 PLIP interactions: 3 interactions with chain C, 5 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: C:N.96, C:E.100, B:H.71 Water bridges: C:Y.122, B:S.63, B:G.94, B:E.100, B:E.100 Salt bridges: K.4 LYS.10: 9 residues within 4Å: Chain B: N.96, E.100 Chain C: S.63, A.64, L.66, H.68, H.71, Y.122 Ligands: LYS.4 8 PLIP interactions: 3 interactions with chain C, 3 Ligand-Ligand interactions, 2 interactions with chain B Hydrogen bonds: C:A.64, C:H.71, C:Y.122, K.4, K.10, B:N.96, B:E.100 Salt bridges: K.10 LYS.13: 11 residues within 4Å: Chain A: N.96, E.100 Chain D: S.63, A.64, L.66, T.67, H.68, H.71, N.96, Y.122 Ligands: LYS.1 8 PLIP interactions: 2 interactions with chain A, 5 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: A:N.96, A:E.100, D:H.71, D:Y.122 Water bridges: D:S.63, D:E.100, D:E.100 Salt bridges: K.13

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

MG.2: 1 residues within 4Å: Chain A: D.239 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.239, A:D.239, H2O.2 MG.3: 3 residues within 4Å: Chain A: Y.149, K.178, N.264 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: R.154, F.260, N.264 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain B: D.239 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.239 MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 6 residues within 4Å: Chain C: G.92, A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP)

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

EDO.5: 5 residues within 4Å: Chain B: I.17, I.18, I.19, D.52, K.88 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.17, B:I.19, B:D.52 EDO.6: 5 residues within 4Å: Chain B: E.203, D.204, A.205, K.257, F.260 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.204, B:A.205 EDO.14: 1 residues within 4Å: Chain D: N.241 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.241 EDO.15: 8 residues within 4Å: Chain D: K.178, G.202, E.203, D.204, I.219, S.220, V.221, F.260 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.204, D:I.219, D:V.221 Water bridges: D:I.219

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

PEG.12: 5 residues within 4Å: Chain C: Q.129, Y.132, D.162, T.163, K.166 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.166

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

PGE.16: 3 residues within 4Å: Chain D: Q.129, Y.132, D.162 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saran, S. et al., B-FACTOR ANALYSIS SUGGEST THAT L-LYSINE AND R, R-BISLYSINE ALLOSTERICALLY INHIBIT Cj.DHDPS ENZYME BY DECREASING PROTEIN DYNAMICS. 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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