SMTL ID : 3d47.5 (4 other biounits)

Crystal structure of L-rhamnonate dehydratase from Salmonella typhimurium complexed with Mg and D-malate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.226, E.252, E.280 Ligands: MLT.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.226, A:E.252, A:E.280, H2O.2 MG.3: 5 residues within 4Å: Chain B: K.189, D.226, E.252, E.280 Ligands: MLT.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.226, B:E.252, B:E.280, H2O.11 MG.5: 5 residues within 4Å: Chain C: K.189, D.226, E.252, E.280 Ligands: MLT.6 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.226, C:E.252, C:E.280, H2O.19 MG.7: 5 residues within 4Å: Chain D: K.189, D.226, E.252, E.280 Ligands: MLT.8 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.226, D:E.252, D:E.280, H2O.28 MG.9: 4 residues within 4Å: Chain E: D.226, E.252, E.280 Ligands: MLT.10 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.226, E:E.252, E:E.280, H2O.36 MG.11: 4 residues within 4Å: Chain F: D.226, E.252, E.280 Ligands: MLT.12 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.226, F:E.252, F:E.280, H2O.43 MG.13: 5 residues within 4Å: Chain G: K.189, D.226, E.252, E.280 Ligands: MLT.14 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.226, G:E.252, G:E.280, H2O.51 MG.15: 5 residues within 4Å: Chain H: K.189, D.226, E.252, E.280 Ligands: MLT.16 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.226, H:E.252, H:E.280, H2O.61

8 x MLT: D-MALATE(Non-covalent)

MLT.2: 12 residues within 4Å: Chain A: H.33, R.59, T.173, K.189, D.226, W.228, E.252, E.280, H.329, E.349, L.351 Ligands: MG.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.173, A:E.280 Water bridges: A:Y.171, A:D.226, A:E.252 Salt bridges: A:H.33, A:R.59, A:K.189, A:H.329 MLT.4: 12 residues within 4Å: Chain B: H.33, R.59, T.173, K.189, D.226, W.228, E.252, E.280, H.329, E.349, L.351 Ligands: MG.3 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.280 Water bridges: B:K.189, B:D.226, B:W.228, B:E.280 Salt bridges: B:H.33, B:R.59, B:K.189, B:H.329 MLT.6: 11 residues within 4Å: Chain C: H.33, R.59, T.173, K.189, D.226, W.228, E.252, E.280, H.329, E.349 Ligands: MG.5 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:E.280 Water bridges: C:K.189, C:D.226, C:E.280 Salt bridges: C:H.33, C:R.59, C:K.189, C:H.329 MLT.8: 12 residues within 4Å: Chain D: H.33, R.59, T.173, K.189, D.226, W.228, E.252, E.280, H.329, E.349, L.351 Ligands: MG.7 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.280 Water bridges: D:K.189, D:D.226 Salt bridges: D:H.33, D:R.59, D:K.189, D:H.329 MLT.10: 12 residues within 4Å: Chain E: H.33, R.59, T.173, K.189, D.226, W.228, E.252, E.280, H.329, E.349, L.351 Ligands: MG.9 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:E.280 Water bridges: E:D.226 Salt bridges: E:H.33, E:R.59, E:K.189, E:H.329 MLT.12: 12 residues within 4Å: Chain F: H.33, R.59, T.173, K.189, D.226, W.228, E.252, E.280, H.329, E.349, L.351 Ligands: MG.11 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:E.280 Water bridges: F:K.189, F:D.226, F:E.252 Salt bridges: F:H.33, F:R.59, F:K.189, F:H.329 MLT.14: 12 residues within 4Å: Chain G: H.33, R.59, T.173, K.189, D.226, W.228, E.252, E.280, H.329, E.349, L.351 Ligands: MG.13 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:E.280 Water bridges: G:K.189, G:D.226, G:W.228 Salt bridges: G:H.33, G:R.59, G:K.189, G:H.329 MLT.16: 12 residues within 4Å: Chain H: H.33, R.59, T.173, K.189, D.226, W.228, E.252, E.280, H.329, E.349, L.351 Ligands: MG.15 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:T.173, H:E.280 Water bridges: H:K.189, H:D.226, H:W.228 Salt bridges: H:H.33, H:R.59, H:K.189, H:H.329

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fedorov, A.A. et al., Crystal structure of L-rhamnonate dehydratase from Salmonella typhimurium complexed with Mg and D-malate. To be Published

Release Date

2008-06-03

Peptides

Putative galactonate dehydratase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Putative galactonate dehydratase

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