SMTL ID : 7knz.2 (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

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

3VN.1: 16 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.68, H.71, N.96, Y.122 Ligands: MG.3, EDO.17 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:H.71, B:N.96, B:Y.122, A:A.64, A:H.71, A:N.96, A:N.96 Water bridges: A:Y.122, A:Y.122

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: D.239 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.239, H2O.3 MG.3: 4 residues within 4Å: Chain A: H.68, S.95, A.100 Ligands: 3VN.1 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain B: L.211, G.214, G.215, K.216, Y.242 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain A: H.68 Chain B: H.68 Ligands: EDO.17 No protein-ligand interaction detected (PLIP)

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

ACT.4: 2 residues within 4Å: Chain A: D.162, D.189 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.161 Salt bridges: A:H.193 ACT.14: 1 residues within 4Å: Chain B: E.76 No protein-ligand interaction detected (PLIP) ACT.15: 3 residues within 4Å: Chain B: I.19, D.52, L.238 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.19 Hydrogen bonds: B:D.52

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

PEG.5: 4 residues within 4Å: Chain A: T.67, H.68, E.69, E.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.67, A:H.68 PEG.6: 3 residues within 4Å: Chain A: I.19, M.198, K.216 No protein-ligand interaction detected (PLIP)

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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.166 Water bridges: A:S.160 PGE.16: 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:D.162, B:K.166 Water bridges: B:S.160

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

EDO.8: 6 residues within 4Å: Chain A: L.211, G.214, G.215, K.216, A.237, Y.242 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.215, A:K.216, A:E.240, A:E.240 EDO.9: 3 residues within 4Å: Chain A: L.274, M.302, I.307 No protein-ligand interaction detected (PLIP) EDO.10: 3 residues within 4Å: Chain A: G.182, E.203, K.257 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.257, A:K.257 EDO.11: 2 residues within 4Å: Chain A: Y.273, F.295 No protein-ligand interaction detected (PLIP) EDO.17: 6 residues within 4Å: Chain B: H.68, S.95, A.97, A.100 Ligands: 3VN.1, MG.13 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:H.99, A:A.64 EDO.18: 1 residues within 4Å: Chain B: K.88 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.88 EDO.19: 4 residues within 4Å: Chain B: K.15, I.17, R.196, M.198 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.15 EDO.20: 4 residues within 4Å: Chain B: M.302, K.303, Y.305, I.307 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.305

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.21: 3 residues within 4Å: Chain B: T.161, D.162, D.189 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.189, B:D.189 Water bridges: B:T.161

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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