SMTL ID : 4fha.1

Structure of Dihydrodipicolinate Synthase from Streptococcus pneumoniae,bound to pyruvate and lysine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-tetramer

Ligands

4 x LYS: LYSINE(Non-covalent)

LYS.1: 10 residues within 4Å: Chain A: S.54, P.55, L.57, H.59, E.62, N.86, Y.113 Chain B: N.86, D.87 Ligands: LYS.3 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A, Hydrogen bonds: B:N.86, B:N.86, A:E.62, A:N.86, A:Y.113 Water bridges: B:D.87, B:D.87 LYS.3: 10 residues within 4Å: Chain A: N.86, D.87 Chain B: S.54, P.55, L.57, H.59, E.62, T.85, Y.113 Ligands: LYS.1 7 PLIP interactions: 1 Ligand-Ligand interactions, 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: K.3, A:N.86, A:N.86, B:P.55, B:E.62 Water bridges: A:D.87, A:D.87 LYS.5: 10 residues within 4Å: Chain C: S.54, P.55, L.57, H.59, E.62, N.86, Y.113 Chain D: N.86, D.87 Ligands: LYS.7 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C, Hydrogen bonds: D:N.86, D:N.86, C:E.62, C:N.86 LYS.7: 10 residues within 4Å: Chain C: N.86, D.87 Chain D: S.54, P.55, L.57, H.59, E.62, T.85, Y.113 Ligands: LYS.5 6 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: D:P.55, D:E.62, D:Y.113, C:N.86, C:N.86, K.7

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

NA.2: 3 residues within 4Å: Chain A: A.159, H.161, I.164 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.161, A:I.164 NA.4: 4 residues within 4Å: Chain B: A.159, D.160, H.161, I.164 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.159, B:I.164 NA.6: 3 residues within 4Å: Chain C: A.159, H.161, I.164 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.164, C:I.164 NA.8: 4 residues within 4Å: Chain D: A.159, D.160, H.161, I.164 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.159, D:I.164

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perugini, M.A. et al., Structure, Function, Stability and Knockout Phenotype of Dihydrodipicolinate Synthase from Streptococcus pneumoniae. To be Published

Release Date

2013-09-18

Peptides

Dihydrodipicolinate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Dihydrodipicolinate synthase

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