SMTL ID : 7kx1.1 (1 other biounit)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, Y110F mutant with pyruvate bound in the active in C2221 space group

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-tetramer

Ligands

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

PGE.1: 6 residues within 4Å: Chain A: Q.128, Q.129, Y.132, D.162, T.163, K.166 No protein-ligand interaction detected (PLIP) PGE.3: 5 residues within 4Å: Chain B: Q.129, Y.132, D.162, T.163, K.166 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.166 Water bridges: B:S.160 PGE.8: 5 residues within 4Å: Chain C: Q.129, Y.132, D.162, T.163, K.166 No protein-ligand interaction detected (PLIP) PGE.12: 5 residues within 4Å: Chain D: Q.129, Y.132, D.162, T.163, K.166 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.162, D:D.162, D:K.166

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: K.247, E.251 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.251 MG.7: 1 residues within 4Å: Chain B: D.239 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.239, H2O.8

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

EDO.4: 8 residues within 4Å: Chain A: Y.208, Y.242, K.243, K.246 Chain B: S.212, E.240, Y.242 Ligands: EDO.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.212, B:E.240, B:E.240, B:Y.242 EDO.5: 9 residues within 4Å: Chain B: L.211, G.214, G.215, K.216, A.237, L.238, E.240, Y.242 Ligands: EDO.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.214, B:G.215, B:K.216 EDO.10: 4 residues within 4Å: Chain C: Y.149, R.154, F.260, N.264 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.154, C:N.264 EDO.13: 5 residues within 4Å: Chain D: P.152, E.158, S.181, N.183, K.186 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.158, D:S.181, D:S.181, D:N.183

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

ACT.6: 2 residues within 4Å: Chain B: H.99 Chain D: L.285 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:H.99 ACT.11: 4 residues within 4Å: Chain C: I.19, G.20, D.52, L.238 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:D.52

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

PEG.9: 7 residues within 4Å: Chain C: L.191, P.195, M.197, G.214, K.216 Chain D: K.246, D.250 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:M.197, D:K.246, D:D.250

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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