SMTL ID : 6ue0.1

Crystal structure of dihydrodipicolinate synthase from Klebsiella pneumoniae bound to pyruvate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-tetramer

Ligands

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: R.172, F.278, P.281, N.282 Chain B: R.143 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.282 Salt bridges: A:R.172, B:R.143 SO4.5: 5 residues within 4Å: Chain A: R.143 Chain B: R.172, F.278, P.281, N.282 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:N.282 Water bridges: B:R.172, A:R.143, A:R.143, A:R.143 Salt bridges: B:R.172, A:R.143 SO4.9: 5 residues within 4Å: Chain C: R.172, F.278, P.281, N.282 Chain D: R.143 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Salt bridges: D:R.143, C:R.172 Hydrogen bonds: C:N.282 SO4.13: 5 residues within 4Å: Chain C: R.143 Chain D: R.172, F.278, P.281, N.282 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:N.282 Water bridges: D:R.172, C:R.143, C:R.143, C:R.143 Salt bridges: D:R.172, C:R.143

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 5 residues within 4Å: Chain A: V.169, P.170, S.171, A.197, T.198 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: G.91, R.125 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: R.264, N.267, Q.268 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain B: G.199, L.201 Chain C: G.199, N.200, L.201 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain B: V.169, P.170, S.171, A.197, T.198 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: R.264, N.267, Q.268 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain C: V.169, P.170, S.171, A.197, T.198 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain C: G.91, R.125 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain C: R.264, N.267, Q.268 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain A: G.199, N.200, L.201 Chain D: G.199, L.201 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain D: V.169, P.170, S.171, A.197, T.198 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain D: R.264, N.267, Q.268 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Impey, R.E. et al., Mis-annotations of a promising antibiotic target in high-priority gram-negative pathogens. Febs Lett. (2020)

Release Date

2020-02-05

Peptides

4-hydroxy-tetrahydrodipicolinate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

C
AAA

D
BBB

4-hydroxy-tetrahydrodipicolinate synthase