SMTL ID : 7kkg.2 (1 other biounit)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, N84D mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

homo-tetramer

Ligands

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

MG.1: 5 residues within 4Å: Chain A: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain A: E.80, K.83 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.80, H2O.7 MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain B: K.109, V.142, D.143 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain B: N.16, I.17, I.18, K.88 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain B: R.154 Chain D: K.125 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) MG.14: 1 residues within 4Å: Chain B: D.239 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.239, H2O.24 MG.15: 2 residues within 4Å: Chain B: E.80, K.83 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.80, H2O.23 MG.16: 2 residues within 4Å: Chain B: E.76, H.111 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.76, B:H.111, H2O.21 MG.25: 5 residues within 4Å: Chain C: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.26: 2 residues within 4Å: Chain C: A.137, Q.140 No protein-ligand interaction detected (PLIP) MG.33: 5 residues within 4Å: Chain D: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.34: 2 residues within 4Å: Chain D: D.52 Ligands: ACT.42 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.52, H2O.43, H2O.47, H2O.50 MG.35: 4 residues within 4Å: Chain D: D.250, E.251, Y.253, N.254 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.250, H2O.39

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 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

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

PEG.6: 4 residues within 4Å: Chain A: G.32, T.67, R.284 Chain C: H.99 No protein-ligand interaction detected (PLIP) PEG.19: 4 residues within 4Å: Chain B: G.32, T.67, R.284 Chain D: H.99 2 PLIP interactions: 2 interactions with chain D Water bridges: D:H.99, D:H.99 PEG.27: 4 residues within 4Å: Chain A: H.99 Chain C: G.32, T.67, R.284 No protein-ligand interaction detected (PLIP) PEG.28: 5 residues within 4Å: Chain C: Q.128, Q.129, Y.132, T.163, K.166 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.166 Water bridges: C:S.160, C:T.163 PEG.36: 5 residues within 4Å: Chain B: H.99 Chain D: G.32, T.67, R.284 Ligands: EDO.38 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.32

4 x LYS: LYSINE(Non-covalent)

LYS.7: 11 residues within 4Å: Chain A: S.63, A.64, L.66, T.67, H.68, H.71, D.96, Y.122 Chain C: D.96, E.100 Ligands: LYS.32 8 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: A:A.64, A:H.71, A:Y.122, C:E.100, K.7 Water bridges: A:S.63, A:D.96 Salt bridges: K.7 LYS.24: 11 residues within 4Å: Chain B: S.63, A.64, L.66, T.67, H.68, H.71, D.96, Y.122 Chain D: D.96, E.100 Ligands: LYS.40 7 PLIP interactions: 5 interactions with chain B, 1 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: B:H.71, B:Y.122, D:E.100 Water bridges: B:S.63, B:E.100, B:E.100 Salt bridges: K.24 LYS.32: 11 residues within 4Å: Chain A: D.96, E.100 Chain C: S.63, A.64, L.66, T.67, H.68, H.71, D.96, Y.122 Ligands: LYS.7 6 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain C, 2 interactions with chain A Salt bridges: K.32 Hydrogen bonds: C:H.71, A:E.100 Water bridges: C:E.100, C:E.100, A:D.96 LYS.40: 10 residues within 4Å: Chain B: D.96, E.100 Chain D: S.63, A.64, L.66, H.68, H.71, D.96, Y.122 Ligands: LYS.24 8 PLIP interactions: 4 interactions with chain D, 2 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: D:A.64, D:H.71, B:D.96, K.40 Water bridges: D:S.63, D:S.63, B:Y.122 Salt bridges: K.40

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain A: K.303, K.304, Y.305, K.306 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.303, A:K.304 Water bridges: A:I.307

2 x NA: SODIUM ION(Non-functional Binders)

NA.17: 3 residues within 4Å: Chain B: T.67, H.68, E.69 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.67, B:H.68, B:E.69 Water bridges: B:E.69 NA.18: 4 residues within 4Å: Chain A: D.185 Chain B: G.182, E.203, I.206 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.203 Water bridges: A:D.185

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

PGE.20: 3 residues within 4Å: Chain B: E.300, K.303, K.304 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.300, B:K.304 Water bridges: B:E.300, B:K.304 PGE.21: 6 residues within 4Å: Chain B: Q.128, Q.129, Y.132, D.162, T.163, K.166 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.162, B:K.166 Water bridges: B:Y.132, B:S.160, B:S.160 PGE.37: 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:D.162, D:K.166 Water bridges: D:Q.129, D:Q.129, D:T.163, D:K.166

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

EDO.22: 4 residues within 4Å: Chain A: D.185 Chain B: A.205, Y.253, K.257 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:Y.253, A:D.185 EDO.23: 3 residues within 4Å: Chain B: E.76, I.77, E.80 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.76 EDO.29: 7 residues within 4Å: Chain C: P.28, F.29, K.30, D.35, S.38, I.278, E.279 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:F.29, C:S.38, C:S.38, C:E.279 Water bridges: C:S.280 EDO.30: 2 residues within 4Å: Chain C: H.193 Chain D: N.254 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.254 EDO.31: 4 residues within 4Å: Chain C: N.254, V.301, K.304, Y.305 1 PLIP interactions: 1 interactions with chain C Water bridges: C:N.254 EDO.38: 4 residues within 4Å: Chain D: T.67, E.70, R.284 Ligands: PEG.36 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.284 EDO.39: 9 residues within 4Å: Chain D: A.24, L.25, V.55, P.56, V.57, G.58, T.60, G.61, K.178 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.25, D:V.57, D:G.58

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

ACT.41: 4 residues within 4Å: Chain C: D.185 Chain D: A.205, Y.253, K.257 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:K.257 Hydrogen bonds: D:Y.253 ACT.42: 6 residues within 4Å: Chain D: I.19, G.20, D.52, H.235, L.238 Ligands: MG.34 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.19, D:L.238 Salt bridges: D:H.235

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
B

B
C

C
E

D
F

4-hydroxy-tetrahydrodipicolinate synthase

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