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

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, E88Q mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 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, H.71, Y.122 Chain B: N.96 Ligands: LYS.13, PGE.23 9 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A, 3 Ligand-Ligand interactions Hydrogen bonds: B:N.96, B:N.96, A:H.71, K.13, K.13 Water bridges: B:Y.122, A:S.63, A:S.63 Salt bridges: K.1 LYS.13: 10 residues within 4Å: Chain A: N.96 Chain B: S.63, A.64, L.66, H.68, H.71, N.96, Y.122 Ligands: LYS.1, PGE.23 10 PLIP interactions: 4 interactions with chain B, 4 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: B:A.64, B:H.71, B:Y.122, K.1, K.1, K.13, A:N.96, A:N.96 Water bridges: B:S.63 Salt bridges: K.13

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: D.239 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.239, H2O.4, H2O.5 MG.3: 5 residues within 4Å: Chain A: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: T.98, H.99 No protein-ligand interaction detected (PLIP) MG.14: 5 residues within 4Å: Chain B: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP)

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

ACT.5: 4 residues within 4Å: Chain A: I.17, I.19, M.198, K.216 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.19, A:K.216 ACT.15: 5 residues within 4Å: Chain B: Y.149, V.151, R.154, K.178, N.264 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.151 Hydrogen bonds: B:N.264 Salt bridges: B:R.154 ACT.16: 2 residues within 4Å: Chain B: I.47, E.48 No protein-ligand interaction detected (PLIP) ACT.17: 5 residues within 4Å: Chain B: D.14, K.15, F.168, R.196 Ligands: EDO.21 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.14 Salt bridges: B:K.15, B:R.196

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

EDO.6: 3 residues within 4Å: Chain A: L.274, M.302, I.307 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.302 EDO.7: 3 residues within 4Å: Chain A: P.152, G.156, C.157 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.152 Water bridges: A:E.158, A:E.158 EDO.8: 3 residues within 4Å: Chain A: T.67, E.69, E.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.67, A:E.69 EDO.9: 4 residues within 4Å: Chain A: T.161, D.162, D.189, H.193 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.193 Water bridges: A:D.162, A:D.162 EDO.18: 3 residues within 4Å: Chain B: K.83, G.84, T.85 No protein-ligand interaction detected (PLIP) EDO.19: 4 residues within 4Å: Chain B: D.162, I.165, K.166, R.169 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.162, B:K.166 Water bridges: B:D.162 EDO.20: 3 residues within 4Å: Chain B: S.291, K.292, E.293 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.292, B:E.293, B:E.293, B:E.293 EDO.21: 7 residues within 4Å: Chain B: K.15, F.168, R.169, D.170, C.171, E.172 Ligands: ACT.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.15, B:E.172

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

PGE.10: 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 PGE.22: 7 residues within 4Å: Chain B: Q.128, Q.129, Y.132, D.162, T.163, K.166 Ligands: PEG.26 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.162, B:K.166 Water bridges: B:Q.129 PGE.23: 12 residues within 4Å: Chain A: H.68, S.95, A.97, H.99, Q.100 Chain B: A.64, T.65, L.66, H.68, Q.100 Ligands: LYS.1, LYS.13 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.95, B:L.66 Water bridges: B:S.95

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

PEG.11: 4 residues within 4Å: Chain A: S.212, G.214, E.240, Y.242 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.240, A:E.240 Water bridges: A:Y.242 PEG.24: 5 residues within 4Å: Chain B: E.251, N.254, V.301, K.304, Y.305 3 PLIP interactions: 3 interactions with chain B Water bridges: B:N.254, B:K.304, B:K.304 PEG.25: 3 residues within 4Å: Chain B: K.243, K.246, K.247 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.243 PEG.26: 4 residues within 4Å: Chain B: K.166, R.169, D.170 Ligands: PGE.22 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.132 Water bridges: B:R.169 PEG.27: 3 residues within 4Å: Chain B: I.19, M.198, K.216 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.216 PEG.28: 6 residues within 4Å: Chain B: R.169, A.192, H.193, E.194, P.195, R.196 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.169, B:R.196 PEG.29: 5 residues within 4Å: Chain B: A.232, H.235, F.236, D.239, N.241 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.236, B:D.239, B:N.241

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 8 residues within 4Å: Chain A: T.59, Y.149, V.151, R.154, K.178, G.202, F.260, N.264 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.154, A:G.202, A:N.264

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saran, S. et al., THE ALLOSTERIC SITE RESIDUE, E88 INTERACTS WITH THE INHIBITORS TO TRANSMIT THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS BY FORMING A HYDROGEN BOND. To Be Published

Release Date

2021-11-17

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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