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

Dihydrodipicolinate synthase from C. jejuni with pyruvate bound to the active site in C2221 space group

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-tetramer

Ligands

4 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.129, A:K.166 PGE.8: 6 residues within 4Å: Chain B: Q.128, Q.129, Y.132, D.162, T.163, K.166 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.166 PGE.17: 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 PGE.20: 6 residues within 4Å: Chain D: Q.128, Q.129, Y.132, D.162, T.163, K.166 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.166

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: D.239 Ligands: ACT.5 No protein-ligand interaction detected (PLIP) GOL.3: 7 residues within 4Å: Chain A: C.82, K.83, G.84, T.85, V.87, K.88, D.114 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.84, A:T.85, A:K.88, A:D.114 GOL.21: 4 residues within 4Å: Chain D: I.51, D.52, K.86, H.235 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:I.51, D:D.52, D:H.235

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

ACT.4: 2 residues within 4Å: Chain A: E.100 Chain C: E.100 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.100 ACT.5: 4 residues within 4Å: Chain A: F.236, D.239, N.241 Ligands: GOL.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.239 Hydrogen bonds: A:D.239, A:N.241 ACT.6: 7 residues within 4Å: Chain A: S.212, G.214, E.240, Y.242 Chain B: Y.208, Y.242, K.246 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.242 Hydrophobic interactions: A:Y.242 ACT.9: 4 residues within 4Å: Chain B: T.161, D.162, D.189, H.193 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.189 Water bridges: B:T.161 ACT.10: 3 residues within 4Å: Chain B: E.100 Chain D: E.100 Ligands: PEG.11 No protein-ligand interaction detected (PLIP) ACT.18: 4 residues within 4Å: Chain C: I.19, G.20, D.52, L.238 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.19 Hydrogen bonds: C:D.52

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

EDO.7: 3 residues within 4Å: Chain A: K.44, E.48, T.81 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.48, A:E.48, A:T.81 EDO.15: 3 residues within 4Å: Chain B: S.181, G.182, E.203 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.181 EDO.16: 2 residues within 4Å: Chain B: P.152, G.156 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.152 Water bridges: B:E.158 EDO.19: 6 residues within 4Å: Chain C: S.212, G.214, Y.242 Chain D: Y.208, K.243, K.246 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.208

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

PEG.11: 8 residues within 4Å: Chain B: A.64, T.65, L.66, R.284 Chain D: A.97, H.99, E.100 Ligands: ACT.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.66 Water bridges: B:R.284 PEG.12: 4 residues within 4Å: Chain B: K.303, K.304, Y.305, K.306 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.303, B:K.306 PEG.22: 3 residues within 4Å: Chain D: I.47, E.48, T.81 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.48, D:E.48

2 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 2 residues within 4Å: Chain B: R.154, N.264 No protein-ligand interaction detected (PLIP) MG.14: 5 residues within 4Å: Chain B: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP)

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

Related Entries With Identical Sequence