SMTL ID : 7jza.1

Dihydrodipicolinate synthase S48F mutant with lysine in the allosteric site, and pyruvate and succinic semi-aldehyde in the catalytic site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-tetramer

Ligands

6 x K: POTASSIUM ION(Non-covalent)

K.1: 4 residues within 4Å: Chain A: A.152, V.154, K.155, I.157 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.152, A:V.154, A:I.157, H2O.9, H2O.10 K.5: 4 residues within 4Å: Chain B: A.152, V.154, K.155, I.157 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.152, B:V.154, B:I.157, H2O.23, H2O.24 K.8: 4 residues within 4Å: Chain B: A.123, E.124, T.126, N.156 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:A.123, B:T.126, H2O.14, H2O.19, H2O.23 K.9: 4 residues within 4Å: Chain C: A.152, V.154, K.155, I.157 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:A.152, C:V.154, C:I.157, H2O.36, H2O.36 K.13: 4 residues within 4Å: Chain D: A.152, V.154, K.155, I.157 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:A.152, D:V.154, D:I.157, H2O.49, H2O.50 K.16: 4 residues within 4Å: Chain D: A.123, E.124, T.126, N.156 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:A.123, D:T.126, H2O.40, H2O.45, H2O.49

4 x LYS: LYSINE(Non-covalent)

LYS.2: 10 residues within 4Å: Chain A: F.48, A.49, L.51, N.52, H.53, H.56, Y.106 Chain B: N.80, E.84 Ligands: LYS.6 10 PLIP interactions: 1 Ligand-Ligand interactions, 6 interactions with chain A, 3 interactions with chain B Water bridges: K.6, A:H.53, A:G.78, A:G.78, A:E.84, B:N.80 Hydrogen bonds: A:H.56, A:Y.106, B:N.80, B:N.80 LYS.6: 10 residues within 4Å: Chain A: N.80, E.84 Chain B: F.48, A.49, L.51, N.52, H.53, H.56, Y.106 Ligands: LYS.2 9 PLIP interactions: 1 Ligand-Ligand interactions, 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: K.6, B:A.49, B:H.56, A:N.80, A:N.80 Water bridges: B:N.80, B:E.84, A:E.84, A:Y.106 LYS.10: 10 residues within 4Å: Chain C: F.48, A.49, L.51, N.52, H.53, H.56, Y.106 Chain D: N.80, E.84 Ligands: LYS.14 8 PLIP interactions: 4 interactions with chain D, 1 Ligand-Ligand interactions, 3 interactions with chain C Hydrogen bonds: D:N.80, D:N.80, C:H.56 Water bridges: D:E.84, D:Y.106, K.14, C:E.84, C:E.84 LYS.14: 10 residues within 4Å: Chain C: N.80, E.84 Chain D: F.48, A.49, L.51, N.52, H.53, H.56, Y.106 Ligands: LYS.10 11 PLIP interactions: 7 interactions with chain D, 2 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: D:A.49, D:H.56, D:Y.106, C:N.80, C:N.80, K.14 Water bridges: D:G.78, D:G.78, D:N.80, D:Y.106, K.10

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: D.58, M.61, M.62 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.58 GOL.4: 2 residues within 4Å: Chain A: S.137 Chain B: R.109 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.137, B:R.109, B:R.109 Water bridges: A:S.137, B:R.109 GOL.7: 3 residues within 4Å: Chain B: I.86, Q.90, H.125 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.125 GOL.11: 3 residues within 4Å: Chain C: D.58, M.61, M.62 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.58 GOL.12: 2 residues within 4Å: Chain C: S.137 Chain D: R.109 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:S.137, D:R.109, D:R.109 Water bridges: C:S.137, D:R.109 GOL.15: 3 residues within 4Å: Chain D: I.86, Q.90, H.125 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Board, A.J. et al., Mapping the uncharted water channel of DHDPS. To Be Published

Release Date

2021-09-22

Peptides

4-hydroxy-tetrahydrodipicolinate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

4-hydroxy-tetrahydrodipicolinate synthase

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