SMTL ID : 7kwp.2 (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, T.67, H.68, H.71, E.100, Y.122 Chain B: N.96, E.100 Ligands: LYS.3 9 PLIP interactions: 5 Ligand-Ligand interactions, 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: K.3, K.3, A:H.71, B:N.96, B:N.96 Water bridges: K.1, K.1, B:Y.122 Salt bridges: K.1 LYS.3: 10 residues within 4Å: Chain A: N.96, E.100 Chain B: S.63, A.64, L.66, H.68, H.71, E.100, Y.122 Ligands: LYS.1 6 PLIP interactions: 2 Ligand-Ligand interactions, 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: K.1, K.1, B:H.71, B:Y.122, B:Y.122, A:N.96 LYS.4: 11 residues within 4Å: Chain C: S.63, A.64, L.66, T.67, H.68, H.71, E.100, Y.122 Chain D: N.96, E.100 Ligands: LYS.6 8 PLIP interactions: 4 Ligand-Ligand interactions, 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: K.6, K.6, C:H.71, C:Y.122, D:N.96, D:N.96 Water bridges: K.4 Salt bridges: K.4 LYS.6: 10 residues within 4Å: Chain C: N.96, E.100 Chain D: S.63, A.64, L.66, H.68, H.71, E.100, Y.122 Ligands: LYS.4 7 PLIP interactions: 2 interactions with chain C, 2 Ligand-Ligand interactions, 3 interactions with chain D Hydrogen bonds: C:N.96, K.4, K.4, D:L.66, D:H.71, D:Y.122 Water bridges: C:Y.122

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

EDO.2: 4 residues within 4Å: Chain A: E.251, N.254, K.304, Y.305 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.254 EDO.5: 4 residues within 4Å: Chain C: E.251, N.254, K.304, Y.305 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.254

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
E

B
F

C
E

D
F

4-hydroxy-tetrahydrodipicolinate synthase

Related Entries With Identical Sequence