SMTL ID : 3vfl.1

Structure, Function, Stability and Knockout Phenotype of Dihydrodipicolinate Synthase from Streptococcus pneumoniae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-tetramer

Ligands

8 x K: POTASSIUM ION(Non-covalent)

K.1: 3 residues within 4Å: Chain A: A.159, H.161, I.164 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:A.159, A:H.161, A:I.164 K.2: 3 residues within 4Å: Chain A: S.54, L.57, E.62 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.54, A:L.57, A:E.62 K.7: 3 residues within 4Å: Chain B: A.159, H.161, I.164 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:A.159, B:H.161, B:I.164 K.8: 3 residues within 4Å: Chain B: S.54, L.57, E.62 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.54, B:L.57, B:E.62, H2O.8 K.11: 3 residues within 4Å: Chain C: A.159, H.161, I.164 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:A.159, C:H.161, C:I.164 K.12: 3 residues within 4Å: Chain C: S.54, L.57, E.62 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:S.54, C:L.57, C:E.62 K.17: 3 residues within 4Å: Chain D: A.159, H.161, I.164 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:A.159, D:H.161, D:I.164 K.18: 3 residues within 4Å: Chain D: S.54, L.57, E.62 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.54, D:L.57, D:E.62, H2O.17

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 12 residues within 4Å: Chain A: A.14, L.46, G.49, T.50, T.51, L.108, Y.140, K.168, I.209 Chain B: Y.114 Ligands: GOL.4, MES.6 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.50, A:T.51, A:T.51, A:T.51, A:K.168, B:Y.114, B:Y.114 Water bridges: A:T.51 GOL.4: 10 residues within 4Å: Chain A: A.48, G.49, T.50, S.54, G.84, L.108, A.109, I.110 Chain B: Y.114 Ligands: GOL.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.54, A:S.54, A:G.84, A:I.110 GOL.5: 8 residues within 4Å: Chain A: T.56, R.273, L.274, L.307, R.308 Chain B: D.87, T.88, R.89 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.56, A:L.274, A:R.308, B:T.88, B:R.89 GOL.9: 10 residues within 4Å: Chain A: Y.114 Chain B: A.14, L.46, G.49, T.50, T.51, L.108, Y.140, K.168 Ligands: MES.10 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.50, B:T.51, B:T.51, B:K.168, B:K.168, A:Y.114 Water bridges: B:A.48, B:T.51, A:Y.114 GOL.13: 12 residues within 4Å: Chain C: A.14, L.46, G.49, T.50, T.51, L.108, Y.140, K.168, I.209 Chain D: Y.114 Ligands: GOL.14, MES.16 8 PLIP interactions: 1 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:Y.114, C:T.50, C:T.50, C:T.51, C:T.51, C:K.168 Water bridges: C:T.51, C:T.51 GOL.14: 10 residues within 4Å: Chain C: A.48, G.49, T.50, S.54, G.84, L.108, A.109, I.110 Chain D: Y.114 Ligands: GOL.13 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:Y.114, C:S.54, C:S.54, C:G.84, C:I.110 GOL.15: 8 residues within 4Å: Chain C: T.56, R.273, L.274, L.307, R.308 Chain D: D.87, T.88, R.89 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:T.56, C:L.274, C:R.308, D:T.88, D:R.89 GOL.19: 10 residues within 4Å: Chain C: Y.114 Chain D: A.14, L.46, G.49, T.50, T.51, L.108, Y.140, K.168 Ligands: MES.20 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:T.50, D:T.50, D:T.51, D:T.51, D:T.51, D:K.168, D:K.168 Water bridges: D:A.48, C:Y.114

4 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.6: 9 residues within 4Å: Chain A: T.50, T.51, Y.140, I.142, R.145, G.192, E.193, F.250 Ligands: GOL.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.50, A:T.51, A:Y.140 Water bridges: A:K.168 Salt bridges: A:R.145, A:K.168 MES.10: 9 residues within 4Å: Chain B: T.50, T.51, Y.140, I.142, R.145, G.192, E.193, F.250 Ligands: GOL.9 6 PLIP interactions: 6 interactions with chain B Water bridges: B:T.51, B:T.51, B:R.145 Salt bridges: B:R.145, B:K.168, B:E.193 MES.16: 9 residues within 4Å: Chain C: T.50, T.51, Y.140, I.142, R.145, G.192, E.193, F.250 Ligands: GOL.13 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.140, C:Y.140 Water bridges: C:T.51, C:R.145, C:K.168 Salt bridges: C:R.145, C:K.168 MES.20: 9 residues within 4Å: Chain D: T.50, T.51, Y.140, I.142, R.145, G.192, E.193, F.250 Ligands: GOL.19 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Y.140 Water bridges: D:R.145, D:K.168 Salt bridges: D:R.145, D:K.168, D:E.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dogovski, C. et al., Structure, Function, Stability and Knockout Phenotype of Dihydrodipicolinate Synthase from Streptococcus pneumoniae. To be Published

Release Date

2013-06-12

Peptides

Dihydrodipicolinate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Dihydrodipicolinate synthase

Related Entries With Identical Sequence