SMTL ID : 7kly.1 (2 other biounits)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59N mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

homo-dimer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 10 residues within 4Å: Chain A: S.63, A.64, L.66, T.67, H.68, N.71, Y.122 Chain B: N.96, E.100 Ligands: LYS.13 9 PLIP interactions: 4 Ligand-Ligand interactions, 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: K.1, K.13, K.13, B:N.96, B:E.100, A:A.64, A:N.71 Salt bridges: K.1 Water bridges: B:Y.122 LYS.13: 10 residues within 4Å: Chain A: N.96, E.100 Chain B: S.63, A.64, L.66, T.67, H.68, N.71, Y.122 Ligands: LYS.1 7 PLIP interactions: 3 Ligand-Ligand interactions, 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: K.1, K.1, B:N.71, B:Y.122, A:N.96, A:E.100 Salt bridges: K.13

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 7 residues within 4Å: Chain A: Q.128, Q.129, Y.132, D.162, T.163, K.166 Ligands: MG.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.166 Water bridges: A:S.160 PG4.14: 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

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

EDO.3: 4 residues within 4Å: Chain A: Y.208, Y.242, K.243, K.246 No protein-ligand interaction detected (PLIP) EDO.4: 5 residues within 4Å: Chain A: S.212, G.214, E.240, Y.242 Ligands: EDO.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.212, A:E.240, A:Y.242 EDO.5: 8 residues within 4Å: Chain A: L.211, G.214, G.215, K.216, A.237, L.238, Y.242 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.215, A:K.216 EDO.6: 3 residues within 4Å: Chain A: P.195, G.214, K.216 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.214 EDO.7: 6 residues within 4Å: Chain A: T.59, Y.149, R.154, K.178, G.202, N.264 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.202, A:N.264 EDO.8: 3 residues within 4Å: Chain A: K.83, G.84, T.85 No protein-ligand interaction detected (PLIP) EDO.15: 5 residues within 4Å: Chain B: D.250, E.251, Y.253, N.254, Y.305 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.253, B:N.254 EDO.16: 4 residues within 4Å: Chain B: C.82, T.85, V.87, D.114 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:C.82, B:D.114 Water bridges: B:G.84, B:D.114 EDO.17: 7 residues within 4Å: Chain B: T.59, Y.149, R.154, K.178, G.202, F.260, N.264 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.202, B:N.264 Water bridges: B:D.204 EDO.18: 6 residues within 4Å: Chain B: I.17, I.18, I.19, D.52, A.53, K.88 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.17, B:I.19, B:D.52 EDO.19: 4 residues within 4Å: Chain B: N.49, G.50, D.228, K.308 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.308 Water bridges: B:S.231 EDO.20: 6 residues within 4Å: Chain B: A.275, G.276, L.277, I.307, K.308, G.309 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.276, B:I.307 Water bridges: B:F.310

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

ACT.9: 2 residues within 4Å: Chain A: R.284 Chain B: H.99 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:H.99, A:R.284 ACT.21: 3 residues within 4Å: Chain B: S.212, G.214, Y.242 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.242 ACT.22: 2 residues within 4Å: Chain B: D.162, D.189 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.189 ACT.23: 3 residues within 4Å: Chain B: P.152, G.156, E.158 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.152 Salt bridges: B:K.125

3 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 4 residues within 4Å: Chain A: D.35, S.38, I.278, E.279 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.38 MG.11: 3 residues within 4Å: Chain A: K.166, D.170 Ligands: PG4.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.170 MG.25: 2 residues within 4Å: Chain B: D.52, K.86 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.52, H2O.9, H2O.9, H2O.12

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 4 residues within 4Å: Chain A: H.68, H.99, E.100, G.103 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.99, A:G.103 Water bridges: A:H.68 GOL.26: 3 residues within 4Å: Chain A: H.99 Chain B: E.70, R.284 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.70

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

PGE.24: 4 residues within 4Å: Chain B: K.44, I.47, E.48, T.81 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.48

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

PEG.27: 2 residues within 4Å: Chain B: F.236, E.244 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saran, S. et al., H59 PLAYS THE MOST VITAL ROLE IN THE TRANSMISSION OF THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS ENZYME. To Be Published

Release Date

2021-11-03

Peptides

4-hydroxy-tetrahydrodipicolinate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

4-hydroxy-tetrahydrodipicolinate synthase

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