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

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H56N mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

4 x LYS: LYSINE(Non-covalent)

LYS.1: 10 residues within 4Å: Chain A: S.63, A.64, L.66, N.68, H.71, N.96, Y.122 Chain B: N.96, E.100 Ligands: LYS.2 8 PLIP interactions: 4 Ligand-Ligand interactions, 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: K.2, K.2, K.2, A:H.71, A:Y.122, B:N.96, B:N.96 Salt bridges: K.1 LYS.2: 9 residues within 4Å: Chain A: N.96, E.100 Chain B: S.63, A.64, L.66, N.68, H.71, Y.122 Ligands: LYS.1 9 PLIP interactions: 2 interactions with chain B, 4 Ligand-Ligand interactions, 3 interactions with chain A Hydrogen bonds: B:S.63, B:H.71, K.1, K.1, A:N.96, A:E.100 Water bridges: K.1, A:Y.122 Salt bridges: K.2 LYS.21: 10 residues within 4Å: Chain C: S.63, A.64, L.66, N.68, H.71, N.96, Y.122 Chain D: N.96, E.100 Ligands: LYS.22 8 PLIP interactions: 4 Ligand-Ligand interactions, 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: K.22, K.22, K.22, D:N.96, D:N.96, C:H.71 Salt bridges: K.21 Water bridges: D:Y.122 LYS.22: 9 residues within 4Å: Chain C: N.96, E.100 Chain D: S.63, A.64, L.66, N.68, H.71, Y.122 Ligands: LYS.21 8 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D, 4 Ligand-Ligand interactions Hydrogen bonds: C:N.96, C:E.100, D:H.71, D:Y.122, K.21, K.21 Water bridges: K.21 Salt bridges: K.22

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

PEG.3: 5 residues within 4Å: Chain A: G.32, K.33, T.67, R.284 Chain B: H.99 No protein-ligand interaction detected (PLIP) PEG.14: 2 residues within 4Å: Chain B: Q.129, E.133 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.129 Water bridges: A:S.289 PEG.15: 5 residues within 4Å: Chain B: S.160, T.161, D.162, D.189, H.193 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.160, B:T.161, B:D.162 Water bridges: B:D.162 PEG.23: 5 residues within 4Å: Chain C: G.32, K.33, T.67, R.284 Chain D: H.99 No protein-ligand interaction detected (PLIP) PEG.34: 2 residues within 4Å: Chain D: Q.129, E.133 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Q.129 Water bridges: C:S.289 PEG.35: 5 residues within 4Å: Chain D: S.160, T.161, D.162, D.189, H.193 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.160, D:T.161, D:D.162 Water bridges: D:T.161

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

EDO.4: 2 residues within 4Å: Chain A: K.303, K.304 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.300, A:K.303 EDO.5: 5 residues within 4Å: Chain A: E.251, N.254, K.304, Y.305 Ligands: EDO.37 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.251, A:N.254, A:Y.305 EDO.6: 5 residues within 4Å: Chain A: R.41, K.44, R.45, E.48, F.310 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.45, A:E.48 EDO.7: 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:L.238 EDO.8: 7 residues within 4Å: Chain A: V.79, C.82, K.83, V.89, G.112, A.113, D.114 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.82, A:V.89, A:D.114 EDO.16: 4 residues within 4Å: Chain B: D.162, I.165, R.169, H.193 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.162, B:R.169, B:R.169 EDO.17: 8 residues within 4Å: Chain B: A.192, H.193 Chain C: D.250, E.251, Y.253, N.254, Y.305 Ligands: EDO.25 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.253, C:N.254, C:Y.305, C:Y.305 EDO.24: 2 residues within 4Å: Chain C: K.303, K.304 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.300, C:K.303 EDO.25: 5 residues within 4Å: Chain C: E.251, N.254, K.304, Y.305 Ligands: EDO.17 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.251, C:N.254 EDO.26: 5 residues within 4Å: Chain C: R.41, K.44, R.45, E.48, F.310 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.45, C:E.48 EDO.27: 7 residues within 4Å: Chain C: L.211, G.214, G.215, K.216, A.237, L.238, Y.242 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.211, C:K.216, C:L.238 EDO.28: 7 residues within 4Å: Chain C: V.79, C.82, K.83, V.89, G.112, A.113, D.114 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:C.82, C:V.89, C:D.114 EDO.36: 4 residues within 4Å: Chain D: D.162, I.165, R.169, H.193 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.162, D:D.162, D:R.169, D:R.169 EDO.37: 8 residues within 4Å: Chain A: D.250, E.251, Y.253, N.254, Y.305 Chain D: A.192, H.193 Ligands: EDO.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.253, A:N.254, A:Y.305

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

ACT.9: 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.10: 3 residues within 4Å: Chain A: K.15, N.16, I.17 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.17 Hydrogen bonds: A:I.17 Salt bridges: A:K.88 ACT.11: 1 residues within 4Å: Chain A: H.99 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:H.99 Water bridges: A:H.99 ACT.12: 3 residues within 4Å: Chain A: I.19, M.198, K.216 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.216 Salt bridges: A:K.216 ACT.18: 6 residues within 4Å: Chain B: L.211, S.212, N.213, G.214, Y.242 Chain C: K.246 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:L.211, B:Y.242 Hydrophobic interactions: C:K.246 Salt bridges: C:K.246 ACT.29: 2 residues within 4Å: Chain C: H.99 Chain D: R.284 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Salt bridges: C:H.99, D:R.284 ACT.30: 3 residues within 4Å: Chain C: K.15, N.16, I.17 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.17 Hydrogen bonds: C:I.17 Salt bridges: C:K.88 ACT.31: 1 residues within 4Å: Chain C: H.99 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:H.99 Water bridges: C:H.99 ACT.32: 3 residues within 4Å: Chain C: I.19, M.198, K.216 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.216 Salt bridges: C:K.216 ACT.38: 6 residues within 4Å: Chain A: K.246 Chain D: L.211, S.212, N.213, G.214, Y.242 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:L.211 Hydrophobic interactions: A:K.246 Salt bridges: A:K.246

4 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 5 residues within 4Å: Chain A: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.19: 5 residues within 4Å: Chain B: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.33: 5 residues within 4Å: Chain C: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.39: 5 residues within 4Å: Chain D: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP)

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

PGE.20: 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:D.162, B:D.162, B:K.166 PGE.40: 6 residues within 4Å: Chain D: Q.128, Q.129, Y.132, D.162, T.163, K.166 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.162, D:K.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saran, S. et al., ALLOSTERIC SITE RESIDUE 'H56' CAPS THE INHIBITOR AT THE TIGHT DIMER INTERFACE FOR TRANSMITTING THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS. To Be Published

Release Date

2021-12-01

Peptides

4-hydroxy-tetrahydrodipicolinate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
B

D
C

4-hydroxy-tetrahydrodipicolinate synthase

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