SMTL ID : 7kn9.3 (2 other biounits)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, E88A mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

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

MG.1: 2 residues within 4Å: Chain A: R.154, N.264 No protein-ligand interaction detected (PLIP) MG.2: 5 residues within 4Å: Chain A: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.10: 6 residues within 4Å: Chain B: A.93, G.94, L.117, S.118, V.119 Ligands: EDO.16 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain B: T.98, H.99 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain B: I.77 No protein-ligand interaction detected (PLIP)

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

PGE.4: 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 PGE.5: 5 residues within 4Å: Chain A: E.251, N.254, V.301, K.304, Y.305 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.251, A:N.254, A:Y.305 PGE.13: 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:K.166 Water bridges: B:Q.129, B:Y.132, B:D.170

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

EDO.6: 3 residues within 4Å: Chain A: C.288, S.289 Chain B: E.133 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.289, B:E.133 EDO.7: 4 residues within 4Å: Chain A: K.303, Y.305, K.306, I.307 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.303, A:I.307, A:I.307 EDO.8: 7 residues within 4Å: Chain A: H.68, S.95, A.97, A.100 Chain B: A.64 Ligands: LYS.9, LYS.24 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.64, A:H.68 EDO.14: 7 residues within 4Å: Chain A: A.64 Chain B: H.68, S.95, A.97, A.100 Ligands: LYS.9, LYS.24 4 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: B:H.68, B:S.95, K.9, A:A.64 EDO.15: 2 residues within 4Å: Chain B: A.192, H.193 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.192 EDO.16: 9 residues within 4Å: Chain B: V.57, G.58, S.63, H.71, G.92, A.93, G.94 Ligands: MG.10, LYS.24 5 PLIP interactions: 1 Ligand-Ligand interactions, 4 interactions with chain B Water bridges: K.24, B:S.63, B:Y.122 Hydrogen bonds: B:S.63, B:G.92 EDO.17: 5 residues within 4Å: Chain B: M.302, K.303, Y.305, K.306, I.307 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.302, B:I.307, B:I.307 EDO.18: 5 residues within 4Å: Chain B: R.41, K.44, R.45, E.48, F.310 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.41, B:E.48 Water bridges: B:N.49 EDO.19: 5 residues within 4Å: Chain A: T.127, Q.129 Chain B: E.262, S.291, N.294 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Water bridges: A:T.127, A:Q.129, B:E.262, B:S.291, B:S.291 Hydrogen bonds: B:N.294

2 x LYS: LYSINE(Non-covalent)

LYS.9: 10 residues within 4Å: Chain A: S.63, A.64, L.66, H.68, H.71, Y.122 Chain B: N.96 Ligands: EDO.8, EDO.14, LYS.24 7 PLIP interactions: 2 Ligand-Ligand interactions, 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: K.9, A:A.64, A:H.71, A:Y.122, B:N.96, B:N.96 Salt bridges: K.9 LYS.24: 12 residues within 4Å: Chain A: N.96 Chain B: S.63, A.64, L.66, H.68, H.71, N.96, Y.122 Ligands: EDO.8, LYS.9, EDO.14, EDO.16 9 PLIP interactions: 2 Ligand-Ligand interactions, 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: K.24, B:S.63, B:H.71, A:N.96, A:N.96, A:N.96 Salt bridges: K.24 Water bridges: B:Y.122, A:Y.122

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

ACT.20: 2 residues within 4Å: Chain B: I.17, K.216 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.216 Salt bridges: B:K.216 ACT.21: 2 residues within 4Å: Chain B: Y.273, L.274 2 PLIP interactions: 2 interactions with chain B Water bridges: B:L.274, B:G.276 ACT.22: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.169

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

PEG.23: 4 residues within 4Å: Chain B: K.136, Q.140, D.170, C.171 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:K.136, B:D.170 Hydrogen bonds: B:Q.140 Water bridges: B:A.139, B:E.172, B:E.172

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
E

B
F

4-hydroxy-tetrahydrodipicolinate synthase

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