SMTL ID : 7kpc.3 (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: 10 residues within 4Å: Chain A: S.63, A.64, L.66, H.68, H.71, N.96, Y.122 Chain B: N.96 Ligands: LYS.12, EDO.18 8 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 4 Ligand-Ligand interactions Hydrogen bonds: B:N.96, B:N.96, A:H.71, K.12, K.12, K.12 Water bridges: B:Y.122 Salt bridges: K.1 LYS.12: 9 residues within 4Å: Chain A: N.96 Chain B: S.63, A.64, L.66, H.68, H.71, Y.122 Ligands: LYS.1, EDO.18 9 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A, 4 Ligand-Ligand interactions Hydrogen bonds: B:H.71, B:Y.122, A:N.96, A:N.96, K.1, K.1, K.1 Water bridges: A:S.95 Salt bridges: K.12

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

MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 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.13: 5 residues within 4Å: Chain B: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP)

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

ACT.4: 8 residues within 4Å: Chain A: T.59, Y.149, V.151, R.154, K.178, G.202, F.260, N.264 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.151 Hydrogen bonds: A:Y.149, A:N.264 Water bridges: A:R.154 Salt bridges: A:R.154 ACT.5: 7 residues within 4Å: Chain A: L.211, G.214, G.215, K.216, A.237, L.238, Y.242 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.216, A:L.238 Hydrogen bonds: A:L.211 Salt bridges: A:K.216 ACT.6: 3 residues within 4Å: Chain A: T.67, R.284 Chain B: H.99 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:H.99 Salt bridges: B:H.99, A:R.284 ACT.14: 3 residues within 4Å: Chain B: K.44, I.47, E.48 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.47, B:E.48 Hydrogen bonds: B:E.48 Water bridges: B:K.44, B:K.44 Salt bridges: B:K.44 ACT.15: 3 residues within 4Å: Chain B: E.48, N.49, G.50 No protein-ligand interaction detected (PLIP)

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

EDO.7: 3 residues within 4Å: Chain A: D.162, I.165, K.166 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.162, A:R.169 EDO.8: 4 residues within 4Å: Chain A: G.276, I.278, E.279, F.310 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.277 EDO.9: 3 residues within 4Å: Chain A: K.308, G.309, F.310 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.309, A:F.310 Water bridges: A:F.310 EDO.10: 4 residues within 4Å: Chain A: K.15, N.16, I.17, K.88 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.16, A:I.17, A:I.17 EDO.16: 4 residues within 4Å: Chain B: L.274, E.299, M.302, K.303 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.299 EDO.17: 3 residues within 4Å: Chain B: P.152, G.156, C.157 No protein-ligand interaction detected (PLIP) EDO.18: 6 residues within 4Å: Chain B: H.68, S.95, A.97, Q.100 Ligands: LYS.1, LYS.12 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.95 Water bridges: B:H.99, A:A.64, A:H.68 EDO.19: 4 residues within 4Å: Chain B: E.251, N.254, K.304, Y.305 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.254 Water bridges: B:N.254 EDO.20: 6 residues within 4Å: Chain B: L.211, G.214, G.215, K.216, A.237, Y.242 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.215, B:K.216

2 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:K.166 Water bridges: A:Q.129 PGE.21: 3 residues within 4Å: Chain B: I.19, M.198, K.216 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.216 Water bridges: B:K.216

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

PEG.22: 5 residues within 4Å: Chain B: Q.128, Q.129, Y.132, D.162, T.163 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.163 Water bridges: B:Q.129, B:Q.129, B:S.160 PEG.23: 7 residues within 4Å: Chain B: V.79, C.82, K.83, T.85, V.87, K.88, D.114 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.79 Water bridges: B:T.85, B:V.89, B:D.114 PEG.24: 3 residues within 4Å: Chain B: E.76, I.77, E.80 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.36 Water bridges: B:E.36

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.25: 8 residues within 4Å: Chain B: T.59, Y.149, V.151, R.154, K.178, G.202, F.260, N.264 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.149, B:R.154, B:R.154, B:G.202, B:N.264 Water bridges: A:K.125

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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