SMTL ID : 7l4b.3 (2 other biounits)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni with pyruvate bound in the active site in P1211 space group

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

homo-tetramer

Ligands

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

PGE.1: 5 residues within 4Å: Chain A: Q.129, Y.132, D.162, T.163, K.166 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.166 PGE.2: 4 residues within 4Å: Chain A: Q.37, A.40, R.41, K.44 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.44 PGE.4: 6 residues within 4Å: Chain B: Q.128, Q.129, Y.132, D.162, T.163, K.166 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.162, B:K.166 PGE.7: 5 residues within 4Å: Chain C: Q.128, Q.129, Y.132, T.163, K.166 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.166 PGE.8: 5 residues within 4Å: Chain D: Q.129, Y.132, D.162, T.163, K.166 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.166

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 1 residues within 4Å: Chain A: R.154 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain B: Y.149, R.154 No protein-ligand interaction detected (PLIP)

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

EDO.6: 3 residues within 4Å: Chain B: T.161, D.162, D.189 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.161, B:D.162

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

ACT.9: 5 residues within 4Å: Chain A: K.125 Chain D: R.154, F.260, S.263, N.264 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D Salt bridges: A:K.125, D:R.154 Hydrophobic interactions: D:F.260, D:N.264

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

2021-12-22

Peptides

4-hydroxy-tetrahydrodipicolinate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
J

C
K

D
L

4-hydroxy-tetrahydrodipicolinate synthase

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