SMTL ID : 7kkd.1 (1 other biounit)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, N84A mutant with pyruvate bound in the active site and R,R-bislysine bound at the allosteric site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

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

3VN.1: 14 residues within 4Å: Chain A: S.63, A.64, L.66, H.68, H.71, E.100, Y.122 Chain D: S.63, A.64, L.66, H.68, H.71, E.100, Y.122 10 PLIP interactions: 5 interactions with chain D, 5 interactions with chain A Hydrogen bonds: D:A.64, D:A.64, D:H.71, D:Y.122, A:A.64, A:A.64, A:H.71 Water bridges: D:S.63, A:G.94, A:Y.122 3VN.9: 14 residues within 4Å: Chain B: S.63, A.64, L.66, H.68, H.71, E.100, Y.122 Chain C: S.63, A.64, L.66, H.68, H.71, E.100, Y.122 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:A.64, B:H.71, B:E.100, C:H.71, C:Y.122 Water bridges: B:E.100, B:Y.122, B:Y.122, B:Y.122, B:Y.122, B:Y.122, C:Y.122

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

MG.2: 5 residues within 4Å: Chain A: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain B: R.169, H.193 Ligands: EDO.19 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain B: K.257, F.260 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Chain B: D.239 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.239, H2O.17, H2O.20 MG.26: 1 residues within 4Å: Chain D: D.52 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.52, H2O.39, H2O.42, H2O.43

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

ACT.3: 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.303 ACT.4: 6 residues within 4Å: Chain A: T.59, V.151, R.154, K.178, G.202, N.264 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain A Water bridges: D:K.125, A:R.154, A:R.154 Salt bridges: D:K.125, A:R.154 Hydrogen bonds: A:N.264 ACT.14: 3 residues within 4Å: Chain B: I.17, M.198, K.216 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.216 ACT.15: 7 residues within 4Å: Chain B: Y.149, V.151, R.154, K.178, G.202, F.260, N.264 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.264 Salt bridges: B:R.154 ACT.21: 7 residues within 4Å: Chain C: Y.149, V.151, R.154, K.178, G.202, F.260, N.264 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.260, C:N.264 Salt bridges: C:R.154 ACT.27: 6 residues within 4Å: Chain D: V.151, R.154, K.178, G.202, F.260, N.264 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:N.264 Salt bridges: D:R.154 Water bridges: A:K.125, A:K.125 ACT.28: 5 residues within 4Å: Chain D: I.19, G.20, D.52, H.235, L.238 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.19, D:L.238 Salt bridges: D:H.235

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

EDO.5: 9 residues within 4Å: Chain A: L.211, G.214, G.215, K.216, A.237, L.238, E.240, Y.242 Ligands: PEG.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.215, A:K.216 EDO.6: 3 residues within 4Å: Chain A: I.47, T.85, K.86 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.86 EDO.16: 3 residues within 4Å: Chain B: H.7, H.10, M.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.10 EDO.17: 3 residues within 4Å: Chain B: T.67, R.284 Chain C: H.99 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.284 EDO.18: 3 residues within 4Å: Chain B: I.19, G.20, D.52 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.19 Water bridges: B:I.19, B:I.19 EDO.19: 5 residues within 4Å: Chain B: D.162, I.165, K.166, R.169 Ligands: MG.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.166, B:R.169 EDO.22: 3 residues within 4Å: Chain C: I.17, M.198, K.216 1 PLIP interactions: 1 interactions with chain C Water bridges: C:K.216 EDO.23: 7 residues within 4Å: Chain C: P.28, F.29, K.30, D.35, S.38, I.278, E.279 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:F.29, C:D.35, C:S.38, C:E.279 Water bridges: C:F.29, C:S.38, C:L.277 EDO.29: 3 residues within 4Å: Chain D: A.232, H.235, F.236 No protein-ligand interaction detected (PLIP)

4 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.162, A:D.162, A:K.166 Water bridges: A:D.170 PGE.20: 6 residues within 4Å: Chain B: Q.128, 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:Y.132 PGE.24: 5 residues within 4Å: Chain C: Q.129, Y.132, D.162, T.163, K.166 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.166 Water bridges: C:Q.129 PGE.30: 6 residues within 4Å: Chain D: Q.128, Q.129, Y.132, D.162, T.163, K.166 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:K.166 Water bridges: D:Q.129, D:Q.129, D:Q.129, D:Q.129, D:S.160

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

PEG.8: 8 residues within 4Å: Chain A: S.212, G.214, E.240, Y.242 Chain B: Y.208, Y.242, K.246 Ligands: EDO.5 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.208, A:E.240, A:Y.242 PEG.25: 1 residues within 4Å: Chain C: E.76 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saran, S. et al., A TIGHT DIMER INTERFACE N84 RESIDUE, PLAYS A CRITICAL ROLE IN THE TRANSMISSION OF THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS. To Be Published

Release Date

2021-11-03

Peptides

4-hydroxy-tetrahydrodipicolinate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
F

4-hydroxy-tetrahydrodipicolinate synthase

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