SMTL ID : 7lbd.2 (1 other biounit)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59K mutant with pyruvate bound in the active site in C2221 space group

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: P.152, G.153, G.156 Chain B: P.152, G.153, G.156 Ligands: PEG.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.153 EDO.2: 6 residues within 4Å: Chain A: S.212, G.214, Y.242 Chain D: Y.208, K.243, K.246 No protein-ligand interaction detected (PLIP) EDO.3: 7 residues within 4Å: Chain A: D.250, E.251, Y.253, N.254, Y.305 Chain D: A.192, H.193 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.250, A:Y.253, A:N.254 Water bridges: A:N.254 EDO.10: 4 residues within 4Å: Chain B: K.15, F.168, R.169, E.172 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.15, B:D.170 EDO.11: 3 residues within 4Å: Chain B: A.232, H.235, F.236 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.239 EDO.15: 7 residues within 4Å: Chain C: P.152, G.153, G.156 Chain D: P.152, G.153, G.156 Ligands: PEG.27 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.153 EDO.16: 6 residues within 4Å: Chain B: Y.208, K.243, K.246 Chain C: S.212, G.214, Y.242 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.242 EDO.17: 7 residues within 4Å: Chain B: A.192, H.193 Chain C: D.250, E.251, Y.253, N.254, Y.305 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.250, C:Y.253, C:N.254, C:Y.305 Water bridges: C:N.254 EDO.24: 4 residues within 4Å: Chain D: K.15, F.168, R.169, E.172 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.15, D:D.170 EDO.25: 3 residues within 4Å: Chain D: A.232, H.235, F.236 No protein-ligand interaction detected (PLIP)

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

PGE.4: 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.18: 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

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

ACT.5: 7 residues within 4Å: Chain A: Y.149, V.151, R.154, K.178, G.202, F.260, N.264 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.151 Hydrogen bonds: A:G.202, A:N.264 Salt bridges: A:R.154 ACT.6: 3 residues within 4Å: Chain A: Y.273, L.274, G.276 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.274 Water bridges: A:G.276, A:G.276 ACT.7: 1 residues within 4Å: Chain A: F.310 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.310 ACT.8: 3 residues within 4Å: Chain A: K.303, Y.305, K.306 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.306 ACT.19: 7 residues within 4Å: Chain C: Y.149, V.151, R.154, K.178, G.202, F.260, N.264 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.151 Hydrogen bonds: C:Y.149, C:G.202, C:N.264 Salt bridges: C:R.154 ACT.20: 3 residues within 4Å: Chain C: Y.273, L.274, G.276 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.274 Water bridges: C:G.276, C:G.276 ACT.21: 1 residues within 4Å: Chain C: F.310 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:F.310 ACT.22: 3 residues within 4Å: Chain C: K.303, Y.305, K.306 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.306

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

PEG.12: 5 residues within 4Å: Chain B: Q.129, Y.132, D.162, T.163, K.166 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.160, B:T.163, B:K.166 Water bridges: B:Q.129, B:S.160 PEG.13: 4 residues within 4Å: Chain B: P.152, G.156, E.158 Ligands: EDO.1 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.158 PEG.14: 4 residues within 4Å: Chain B: V.34, D.35, E.36, Q.37 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.36, B:Q.37 PEG.26: 5 residues within 4Å: Chain D: Q.129, Y.132, D.162, T.163, K.166 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.160, D:K.166 Water bridges: D:Q.129, D:S.160 PEG.27: 4 residues within 4Å: Chain D: P.152, G.156, E.158 Ligands: EDO.15 1 PLIP interactions: 1 interactions with chain D Water bridges: D:E.158 PEG.28: 4 residues within 4Å: Chain D: V.34, D.35, E.36, Q.37 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.35, D:E.36, D:Q.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yazdi, M.M. et al., Reversing the roles of a crucial hydrogen-bonding pair: a lysine-insensitive mutant of Campylobacter jejuni dihydrodipicolinate synthase, H59K, binds histidine in its allosteric site. To Be Published

Release Date

2022-01-12

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