SMTL ID : 7kn9.2 (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

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

MG.1: 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.5, H2O.5 MG.2: 1 residues within 4Å: Chain A: D.114 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.114, H2O.1 MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: C.288, S.289 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain A: K.83, G.84 No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain A: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.17: 5 residues within 4Å: Chain B: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

PGE.7: 5 residues within 4Å: Chain A: Q.129, Y.132, D.162, T.163, K.166 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.166 PGE.19: 6 residues within 4Å: Chain B: Q.128, Q.129, Y.132, D.162, T.163, K.166 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.166

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

EDO.8: 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:S.212, A:E.240, A:Y.242 EDO.9: 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:G.214, A:G.215, A:K.216 EDO.10: 4 residues within 4Å: Chain A: P.152, G.156, C.157, E.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.152 Water bridges: A:E.158 EDO.11: 8 residues within 4Å: Chain A: T.59, Y.149, R.154, K.178, G.202, F.260, N.264 Ligands: PEG.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.149, A:R.154, A:G.202, A:N.264 EDO.12: 3 residues within 4Å: Chain A: T.127, Q.128 Chain B: E.262 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.262, A:Q.128 Water bridges: B:S.263, B:N.294, B:N.294, A:Q.128, A:Q.129 EDO.20: 3 residues within 4Å: Chain B: I.19, M.198, K.216 No protein-ligand interaction detected (PLIP) EDO.21: 3 residues within 4Å: Chain B: S.212, G.214, Y.242 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.242 Water bridges: B:L.211, B:K.216, B:K.216 EDO.22: 3 residues within 4Å: Chain A: L.285 Chain B: T.98, H.99 No protein-ligand interaction detected (PLIP) EDO.23: 5 residues within 4Å: Chain B: C.82, T.85, V.87, K.88, D.114 No protein-ligand interaction detected (PLIP)

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

ACT.13: 7 residues within 4Å: Chain A: H.68, S.95, A.97, A.100 Chain B: A.64 Ligands: LYS.16, LYS.27 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.95 Salt bridges: A:H.68, A:H.99 ACT.14: 4 residues within 4Å: Chain A: I.17, I.19, M.198, K.216 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.19, A:K.216 Salt bridges: A:K.216 ACT.24: 3 residues within 4Å: Chain B: K.15, F.168, R.196 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.15, B:R.196 ACT.25: 2 residues within 4Å: Chain B: Y.273, L.274 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Y.273, B:G.276 ACT.26: 6 residues within 4Å: Chain A: A.64 Chain B: H.68, A.97, A.100 Ligands: LYS.16, LYS.27 7 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B, 3 Ligand-Ligand interactions Hydrogen bonds: A:A.64, B:S.95, K.16 Hydrophobic interactions: B:A.100 Salt bridges: B:H.68 Water bridges: K.27, K.27

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

PEG.15: 7 residues within 4Å: Chain A: R.154, F.260, E.262, S.263, N.264 Chain B: K.125 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.154, A:N.264

2 x LYS: LYSINE(Non-covalent)

LYS.16: 10 residues within 4Å: Chain A: S.63, A.64, L.66, H.68, H.71, Y.122 Chain B: N.96 Ligands: ACT.13, ACT.26, LYS.27 9 PLIP interactions: 4 Ligand-Ligand interactions, 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: K.16, K.27, A:A.64, A:H.71, A:Y.122, B:N.96, B:N.96 Water bridges: K.27 Salt bridges: K.16 LYS.27: 11 residues within 4Å: Chain A: N.96 Chain B: S.63, A.64, L.66, H.68, H.71, N.96, Y.122 Ligands: ACT.13, LYS.16, ACT.26 9 PLIP interactions: 1 interactions with chain B, 5 Ligand-Ligand interactions, 3 interactions with chain A Hydrogen bonds: B:H.71, K.16, K.16, A:N.96, A:N.96 Water bridges: K.27, K.27, A:Y.122 Salt bridges: K.27

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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