SMTL ID : 7knz.1 (2 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

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.1, H2O.3 MG.2: 1 residues within 4Å: Chain A: K.83 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain B: D.52, H.235 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.52, H2O.11 MG.16: 1 residues within 4Å: Chain A: T.67 No protein-ligand interaction detected (PLIP)

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

ACT.3: 5 residues within 4Å: Chain A: H.68, A.97, A.100 Chain B: A.64 Ligands: 3VN.14 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.97, A:A.100 Salt bridges: A:H.68 ACT.4: 2 residues within 4Å: Chain A: R.41, F.310 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.41 Salt bridges: A:R.41 ACT.5: 3 residues within 4Å: Chain A: K.308, G.309, F.310 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.309 Salt bridges: A:K.308 ACT.17: 5 residues within 4Å: Chain B: H.68, S.95, A.97, A.100 Ligands: 3VN.14 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.97, B:A.100 Water bridges: B:H.99 Salt bridges: B:H.68

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

PEG.6: 4 residues within 4Å: Chain A: L.191, P.195, G.214, K.216 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.191, A:G.214

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

PGE.7: 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.18: 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:K.166 Water bridges: B:Q.129, B:D.170

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

EDO.8: 3 residues within 4Å: Chain A: P.290, K.292, F.295 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.290 EDO.9: 5 residues within 4Å: Chain A: D.250, E.251, Y.253, N.254, Y.305 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.253, A:N.254, A:N.254, A:Y.305 EDO.10: 4 residues within 4Å: Chain A: K.303, K.304, Y.305, K.306 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.304 EDO.11: 1 residues within 4Å: Chain A: H.193 No protein-ligand interaction detected (PLIP) EDO.12: 3 residues within 4Å: Chain A: E.133 Chain B: C.288, S.289 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:E.133 Hydrogen bonds: B:S.289, B:S.289 EDO.13: 2 residues within 4Å: Chain A: T.127, Q.128 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.128 Water bridges: A:T.127, B:N.294 EDO.19: 9 residues within 4Å: Chain B: K.178, G.202, E.203, D.204, I.219, S.220, V.221, F.260 Ligands: EDO.20 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.204, B:I.219, B:V.221 Water bridges: B:E.203 EDO.20: 5 residues within 4Å: Chain B: E.203, D.204, A.205, F.260 Ligands: EDO.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.205 Water bridges: B:K.257 EDO.21: 5 residues within 4Å: Chain B: V.34, E.36, E.69, E.70, T.73 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.73 EDO.22: 1 residues within 4Å: Chain B: N.254 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.254 EDO.23: 2 residues within 4Å: Chain A: H.99 Chain B: R.284 No protein-ligand interaction detected (PLIP) EDO.24: 8 residues within 4Å: Chain B: L.211, G.214, G.215, K.216, A.237, L.238, E.240, Y.242 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.214, B:G.214, B:K.216, B:L.238, B:Y.242

1 x 3VN: (2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid(Non-covalent)

3VN.14: 16 residues within 4Å: Chain A: S.63, A.64, L.66, T.67, H.68, H.71, N.96, Y.122 Chain B: S.63, A.64, L.66, H.71, N.96, Y.122 Ligands: ACT.3, ACT.17 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.64, A:H.71, A:N.96, A:N.96, B:H.71, B:N.96, B:Y.122 Water bridges: A:Y.122

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
A

B
D

4-hydroxy-tetrahydrodipicolinate synthase

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