SMTL ID : 7kly.2 (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: 9 residues within 4Å: Chain A: S.63, A.64, L.66, H.68, N.71, Y.122 Chain B: N.96, E.100 Ligands: LYS.15 7 PLIP interactions: 3 interactions with chain B, 3 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: B:N.96, B:E.100, K.15, K.15, A:N.71 Water bridges: B:Y.122 Salt bridges: K.1 LYS.15: 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 9 PLIP interactions: 4 Ligand-Ligand interactions, 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: K.1, K.1, K.15, B:A.64, B:N.71, B:Y.122, A:N.96, A:E.100 Salt bridges: K.15

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

PG4.2: 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:Q.129 PG4.16: 6 residues within 4Å: Chain B: Q.128, Q.129, Y.132, D.162, T.163, K.166 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.129, B:K.166 Water bridges: B:Q.129, B:S.160

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

EDO.3: 7 residues within 4Å: Chain A: T.59, Y.149, R.154, K.178, G.202, F.260, N.264 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.202, A:N.264 EDO.4: 6 residues within 4Å: Chain A: D.250, E.251, Y.253, N.254, K.304, Y.305 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.253, A:N.254, A:K.304 EDO.5: 8 residues within 4Å: Chain A: L.211, G.214, G.215, K.216, A.237, L.238, Y.242 Ligands: PGE.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.215, A:K.216 EDO.17: 4 residues within 4Å: Chain B: C.82, T.85, K.86, V.87 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.82 Water bridges: B:T.85 EDO.18: 3 residues within 4Å: Chain B: D.52, K.86 Ligands: ACT.24 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.52, B:D.52 EDO.19: 6 residues within 4Å: Chain B: Y.149, R.154, K.178, G.202, F.260, N.264 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.202, B:N.264 EDO.20: 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:Y.242 EDO.21: 3 residues within 4Å: Chain B: K.15, F.168, R.196 No protein-ligand interaction detected (PLIP) EDO.22: 3 residues within 4Å: Chain B: S.212, G.214, Y.242 No protein-ligand interaction detected (PLIP) EDO.23: 4 residues within 4Å: Chain B: K.125, P.126, T.127, Q.128 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.125, B:P.126, B:Q.128 Water bridges: B:Q.128

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

ACT.6: 3 residues within 4Å: Chain A: L.274, M.302, I.307 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.274 ACT.24: 5 residues within 4Å: Chain B: G.20, D.52, H.235, L.238 Ligands: EDO.18 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.238 Water bridges: B:I.19, B:H.235 ACT.25: 3 residues within 4Å: Chain A: L.285 Chain B: T.98, H.99 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:H.99 Water bridges: B:H.99, A:L.285 ACT.26: 2 residues within 4Å: Chain A: H.99 Chain B: R.284 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.284, A:H.99 ACT.27: 1 residues within 4Å: Chain B: K.106 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.106 Salt bridges: B:K.106

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

PGE.7: 6 residues within 4Å: Chain A: I.17, I.19, M.198, K.216, L.238 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.216 Water bridges: A:P.195 PGE.28: 7 residues within 4Å: Chain B: K.109, A.139, Q.140, S.141, V.142, D.143, N.173 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.139, B:N.173 PGE.29: 3 residues within 4Å: Chain B: H.235, F.236, D.239 2 PLIP interactions: 2 interactions with chain B Water bridges: B:H.235, B:D.239

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

MG.8: 2 residues within 4Å: Chain A: C.288, S.289 No protein-ligand interaction detected (PLIP) MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Chain A: D.239 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.239, H2O.1, H2O.4, H2O.5 MG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain A: D.114 No protein-ligand interaction detected (PLIP) MG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.30: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 4 residues within 4Å: Chain A: D.162, I.165, K.166, R.169 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.162, A:K.166, A:R.169

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

PEG.31: 4 residues within 4Å: Chain B: I.19, M.198, K.216, L.238 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.238

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
C

4-hydroxy-tetrahydrodipicolinate synthase

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