SMTL ID : 7klt.2 (2 other biounits)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59N mutant with pyruvate bound in the active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

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

PG4.1: 6 residues within 4Å: Chain A: Q.128, Q.129, Y.132, D.162, T.163, K.166 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.166 Water bridges: A:T.163 PG4.14: 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

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: D.239 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.239, H2O.1

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

EDO.3: 6 residues within 4Å: Chain A: P.126, T.127, Q.128, C.157, E.158 Ligands: EDO.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.128, A:E.158 Water bridges: A:Q.128 EDO.4: 3 residues within 4Å: Chain A: S.212, E.240, Y.242 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.212, A:E.240, A:Y.242 EDO.5: 3 residues within 4Å: Chain A: K.44, I.47, E.48 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.44 EDO.6: 4 residues within 4Å: Chain A: E.262, S.291, N.294 Chain B: T.127 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:T.127, B:Q.128 Hydrogen bonds: A:N.294 EDO.7: 3 residues within 4Å: Chain A: K.83, G.84, T.85 No protein-ligand interaction detected (PLIP) EDO.8: 3 residues within 4Å: Chain A: P.152, G.156 Ligands: EDO.3 No protein-ligand interaction detected (PLIP) EDO.9: 4 residues within 4Å: Chain A: V.34, D.35, E.36, Q.37 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.34, A:E.36, A:Q.37 EDO.15: 5 residues within 4Å: Chain B: F.29, G.32, E.282, F.283, R.284 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.32, B:E.282, B:R.284 EDO.16: 6 residues within 4Å: Chain B: D.250, E.251, L.252, Y.253, N.254, Y.305 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.254, B:Y.305 EDO.17: 6 residues within 4Å: Chain A: K.125 Chain B: R.154, F.260, E.262, S.263, N.264 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.154, B:E.262, B:N.264 EDO.18: 4 residues within 4Å: Chain B: G.20, D.52, H.235, L.238 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.235

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

ACT.10: 7 residues within 4Å: Chain A: V.57, S.63, N.71, G.92, A.93, G.94, L.104 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.57 Hydrogen bonds: A:V.57, A:S.63, A:G.94 Water bridges: A:A.93 ACT.11: 7 residues within 4Å: Chain A: Y.149, V.151, R.154, K.178, G.202, F.260, N.264 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.264 Salt bridges: A:R.154 ACT.20: 2 residues within 4Å: Chain B: M.198, K.216 No protein-ligand interaction detected (PLIP) ACT.21: 5 residues within 4Å: Chain B: T.59, Y.149, R.154, K.178, N.264 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.264 Salt bridges: B:R.154

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 7 residues within 4Å: Chain A: L.211, G.214, G.215, K.216, A.237, L.238, Y.242 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.211, A:K.216, A:A.237 GOL.13: 3 residues within 4Å: Chain A: T.161, D.162, D.189 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.162, A:D.189 Water bridges: A:T.161, A:T.161

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

PGE.19: 4 residues within 4Å: Chain B: K.44, I.47, E.48, T.81 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.44, B:E.48

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
B

B
D

4-hydroxy-tetrahydrodipicolinate synthase

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