SMTL ID : 7kuz.1 (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: 9 residues within 4Å: Chain A: S.63, A.64, L.66, H.71, Y.122 Chain D: N.96, E.100 Ligands: MG.10, LYS.34 9 PLIP interactions: 2 interactions with chain D, 4 interactions with chain A, 3 Ligand-Ligand interactions Hydrogen bonds: D:N.96, D:E.100, A:H.71, A:Y.122 Water bridges: A:E.100, A:Y.122, K.1, K.1 Salt bridges: K.1 LYS.14: 9 residues within 4Å: Chain B: S.63, A.64, L.66, N.68, H.71, Y.122 Chain C: N.96, E.100 Ligands: LYS.24 8 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C, 3 Ligand-Ligand interactions Hydrogen bonds: B:A.64, B:H.71, B:Y.122, C:N.96, C:E.100, K.14 Water bridges: K.14 Salt bridges: K.14 LYS.24: 8 residues within 4Å: Chain B: N.96, E.100 Chain C: S.63, A.64, L.66, H.71, Y.122 Ligands: LYS.14 9 PLIP interactions: 3 interactions with chain B, 5 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: B:N.96, B:E.100, C:S.63, C:H.71 Water bridges: B:Y.122, C:S.63, C:E.100, C:E.100 Salt bridges: K.24 LYS.34: 9 residues within 4Å: Chain A: N.96, E.100 Chain D: S.63, A.64, L.66, N.68, H.71, Y.122 Ligands: LYS.1 9 PLIP interactions: 3 interactions with chain A, 3 interactions with chain D, 3 Ligand-Ligand interactions Hydrogen bonds: A:N.96, A:E.100, D:S.63, D:A.64, D:H.71, K.34 Water bridges: A:Y.122, K.34 Salt bridges: K.34

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

PEG.2: 3 residues within 4Å: Chain A: G.32, R.284 Chain D: H.99 No protein-ligand interaction detected (PLIP) PEG.25: 4 residues within 4Å: Chain B: H.99 Chain C: G.32, K.33, T.67 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:K.33 Water bridges: B:H.99 PEG.26: 8 residues within 4Å: Chain B: T.127, Q.129 Chain C: E.262, C.288, S.289, P.290, S.291, N.294 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.289, C:S.291, C:N.294, B:T.127 PEG.27: 5 residues within 4Å: Chain C: Q.128, Q.129, Y.132, T.163, K.166 2 PLIP interactions: 2 interactions with chain C Water bridges: C:S.160, C:S.160 PEG.35: 2 residues within 4Å: Chain D: R.41, F.310 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.41, D:R.41 PEG.36: 5 residues within 4Å: Chain C: Y.253, K.257 Chain D: D.162, D.189, H.193 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.253, C:Y.253 PEG.37: 5 residues within 4Å: Chain D: Q.129, Y.132, D.162, T.163, K.166 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.166

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

EDO.3: 3 residues within 4Å: Chain A: D.162, D.189, H.193 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.162 Water bridges: A:D.189, B:Y.253 EDO.4: 3 residues within 4Å: Chain A: G.103, K.106, F.107 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.103, A:F.107 EDO.5: 4 residues within 4Å: Chain A: M.302, Y.305, K.306, I.307 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.302, A:I.307, A:I.307 EDO.6: 3 residues within 4Å: Chain A: R.169, E.194, R.196 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.169, A:E.194, A:R.196 EDO.15: 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:G.215, B:K.216 EDO.16: 3 residues within 4Å: Chain B: K.125, G.156 Chain C: G.153 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Water bridges: C:G.153 Hydrogen bonds: B:G.156 EDO.17: 1 residues within 4Å: Chain B: K.106 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.106 EDO.18: 3 residues within 4Å: Chain B: T.67, R.284 Chain C: H.99 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.284 EDO.28: 5 residues within 4Å: Chain C: L.191, P.195, G.214 Chain D: K.246, D.250 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:K.246, D:D.250, C:G.214 EDO.29: 8 residues within 4Å: Chain C: L.211, G.214, G.215, K.216, A.237, L.238, E.240, Y.242 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.214, C:G.215, C:K.216, C:Y.242 EDO.38: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.39: 5 residues within 4Å: Chain D: E.69, R.72, T.73, E.76, F.107 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.69, D:T.73, D:E.76 EDO.40: 4 residues within 4Å: Chain D: A.275, G.276, G.309, F.310 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.276 Water bridges: D:F.310, D:F.310 EDO.41: 3 residues within 4Å: Chain D: Q.140, S.141, V.142 No protein-ligand interaction detected (PLIP)

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

ACT.7: 1 residues within 4Å: Chain A: Y.273 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.273, A:Y.273 ACT.19: 4 residues within 4Å: Chain B: F.283, R.284, L.285 Ligands: PGE.33 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.284 Hydrogen bonds: B:L.285 ACT.30: 3 residues within 4Å: Chain C: I.19, D.52, L.238 No protein-ligand interaction detected (PLIP) ACT.42: 2 residues within 4Å: Chain D: E.76, H.111 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:H.111

10 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 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.2, H2O.4, H2O.5 MG.9: 5 residues within 4Å: Chain A: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain A: G.94, L.104 Ligands: LYS.1 No protein-ligand interaction detected (PLIP) MG.20: 5 residues within 4Å: Chain B: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain B: R.169, H.193 No protein-ligand interaction detected (PLIP) MG.22: 1 residues within 4Å: Chain B: K.83 No protein-ligand interaction detected (PLIP) MG.31: 4 residues within 4Å: Chain C: A.93, G.94, L.117, V.119 No protein-ligand interaction detected (PLIP) MG.32: 1 residues within 4Å: Chain C: Y.273 No protein-ligand interaction detected (PLIP) MG.43: 5 residues within 4Å: Chain D: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.44: 6 residues within 4Å: Chain D: E.179, A.180, S.181, G.182, E.203, I.206 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.179, D:E.203, H2O.25

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

PGE.11: 5 residues within 4Å: Chain A: Q.129, Y.132, D.162, T.163, K.166 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.162, A:K.166 PGE.12: 3 residues within 4Å: Chain A: E.300, K.303, K.304 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.300, A:E.300 PGE.23: 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:T.163, B:K.166 Water bridges: B:S.160 PGE.33: 6 residues within 4Å: Chain C: T.98, H.99, V.102, G.103, K.106 Ligands: ACT.19 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.103, C:K.106 Water bridges: C:H.99

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 6 residues within 4Å: Chain A: C.82, K.83, T.85, V.87, K.88, D.114 3 PLIP interactions: 3 interactions with chain A Water bridges: A:C.82, A:D.114, A:D.114

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
A

B
D

C
E

D
F

4-hydroxy-tetrahydrodipicolinate synthase

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