SMTL ID : 7jzb.1

Dihydrodipicolinate synthase S48W with lysine in the allosteric site, and pyruvate and succinic semi-aldehyde

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-tetramer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 4 residues within 4Å: Chain A: A.152, V.154, K.155, I.157 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.152, A:V.154, A:I.157, H2O.8, H2O.8 K.2: 4 residues within 4Å: Chain B: A.152, V.154, K.155, I.157 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.152, B:V.154, B:I.157, H2O.15 K.4: 4 residues within 4Å: Chain C: A.152, V.154, K.155, I.157 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:A.152, C:V.154, C:I.157, H2O.23, H2O.23 K.5: 4 residues within 4Å: Chain D: A.152, V.154, K.155, I.157 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:A.152, D:V.154, D:I.157, H2O.30

2 x LYS: LYSINE(Non-covalent)

LYS.3: 6 residues within 4Å: Chain A: A.49, N.80, Y.106 Chain B: A.49, N.80, Y.106 11 PLIP interactions: 4 interactions with chain B, 2 Ligand-Ligand interactions, 5 interactions with chain A Hydrophobic interactions: B:Y.106, A:Y.106 Hydrogen bonds: B:N.80, B:Y.106, B:Y.106, A:A.49, A:N.80 Water bridges: K.3, K.3, A:N.80, A:N.80 LYS.6: 6 residues within 4Å: Chain C: A.49, N.80, Y.106 Chain D: A.49, N.80, Y.106 10 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: C:Y.106, D:Y.106 Hydrogen bonds: C:A.49, C:N.80, D:N.80, D:Y.106 Water bridges: C:N.80, C:N.80, K.6, K.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Board, A.J. et al., Mapping the uncharted water channel of DHDPS. To Be Published

Release Date

2021-09-22

Peptides

4-hydroxy-tetrahydrodipicolinate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

4-hydroxy-tetrahydrodipicolinate synthase