SMTL ID : 7km1.1 (2 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.166 PG4.2: 8 residues within 4Å: Chain A: I.19, P.195, M.197, M.198, G.214, K.216, L.238 Ligands: EDO.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.214, A:L.238 Water bridges: A:K.216

1 x 3VN: (2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid(Non-covalent)

3VN.3: 18 residues within 4Å: Chain A: S.63, A.64, L.66, T.67, H.68, N.71, N.96, E.100, Y.122 Chain B: S.63, A.64, L.66, H.68, N.71, N.96, E.100, Y.122 Ligands: EDO.4 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:N.71, A:N.96, A:N.96, A:N.96, B:N.71, B:N.96, B:N.96, B:E.100, B:Y.122 Water bridges: A:G.94, A:Y.122

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

EDO.4: 5 residues within 4Å: Chain A: H.68, E.100 Chain B: H.68, E.100 Ligands: 3VN.3 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.100 Water bridges: B:E.100 EDO.5: 8 residues within 4Å: Chain A: L.211, G.214, G.215, K.216, A.237, L.238, Y.242 Ligands: PG4.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.215, A:K.216 Water bridges: A:K.216 EDO.14: 6 residues within 4Å: Chain A: K.125 Chain B: R.154, F.260, S.263, N.264 Ligands: ACT.22 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.154, B:N.264 EDO.15: 5 residues within 4Å: Chain B: E.48, N.49, K.308, G.309, F.310 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.49, B:K.308, B:G.309 EDO.16: 3 residues within 4Å: Chain A: Q.129 Chain B: E.262, S.291 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:T.127, A:T.127, B:P.290 Hydrogen bonds: B:S.291 EDO.17: 7 residues within 4Å: Chain B: L.211, G.214, G.215, K.216, A.237, L.238, Y.242 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.211, B:K.216 EDO.18: 6 residues within 4Å: Chain B: D.250, E.251, Y.253, N.254, K.304, Y.305 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.253, B:N.254, B:N.254, B:N.254, B:K.304, B:Y.305 EDO.19: 3 residues within 4Å: Chain B: S.212, E.240, Y.242 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.240, B:Y.242

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

PEG.6: 3 residues within 4Å: Chain A: K.308, G.309, F.310 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.309 Water bridges: A:F.310, A:F.310 PEG.7: 2 residues within 4Å: Chain A: V.102, K.106 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.140 PEG.8: 3 residues within 4Å: Chain A: E.48, N.49, G.50 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.86

4 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain A: D.162, I.165 No protein-ligand interaction detected (PLIP) MG.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.21: 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.7

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

ACT.11: 2 residues within 4Å: Chain A: G.112, D.114 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.114, A:D.114 ACT.12: 3 residues within 4Å: Chain A: S.212, G.214, Y.242 No protein-ligand interaction detected (PLIP) ACT.22: 7 residues within 4Å: Chain B: T.59, Y.149, R.154, K.178, F.260, N.264 Ligands: EDO.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.264 Salt bridges: B:R.154

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

PGE.13: 6 residues within 4Å: Chain B: Q.128, Q.129, Y.132, D.162, T.163, K.166 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.166 Water bridges: B:K.166, B:K.166

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

2021-11-17

Peptides

4-hydroxy-tetrahydrodipicolinate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

4-hydroxy-tetrahydrodipicolinate synthase

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