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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-dimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 1 residues within 4Å: Chain A: D.239 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.239, H2O.2, H2O.3, H2O.4 MG.6: 5 residues within 4Å: Chain B: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain B: D.52 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.52, H2O.10, H2O.11, H2O.12

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

ACT.2: 3 residues within 4Å: Chain A: N.256, K.257, F.260 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.257 Salt bridges: A:K.257 ACT.9: 4 residues within 4Å: Chain B: I.19, D.52, H.235, L.238 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.19, B:L.238 Salt bridges: B:H.235

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

EDO.3: 4 residues within 4Å: Chain A: K.303, K.304, Y.305, K.306 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.304, A:K.306

1 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.163, A:K.166 Water bridges: A:S.160

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

3VN.5: 13 residues within 4Å: Chain A: S.63, A.64, L.66, H.68, H.71, N.96, Y.122 Chain B: S.63, A.64, L.66, H.71, N.96, Y.122 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:A.64, A:H.71, A:N.96, A:N.96, A:N.96, B:H.71, B:N.96, B:N.96, B:Y.122 Water bridges: A:S.95

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

PEG.8: 5 residues within 4Å: Chain B: Q.129, Y.132, D.162, T.163, K.166 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.166 Water bridges: B:Q.129

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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