SMTL ID : 3cxo.2 (1 other biounit)

Crystal structure of L-rhamnonate dehydratase from Salmonella typhimurium complexed with Mg and 3-deoxy-L-rhamnonate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-octamer

Ligands

4 x 3LR: 3,6-dideoxy-L-arabino-hexonic acid(Non-covalent)

3LR.1: 15 residues within 4Å: Chain A: H.35, W.42, I.47, R.61, T.175, K.191, P.193, D.228, W.230, E.254, E.282, H.331, E.351, L.353 Ligands: MG.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.42, A:P.193, A:L.353 Hydrogen bonds: A:H.35, A:R.61, A:R.61, A:T.175, A:E.282 Water bridges: A:K.191, A:D.228 Salt bridges: A:K.191, A:H.331 3LR.5: 15 residues within 4Å: Chain C: H.35, W.42, I.47, R.61, T.175, K.191, P.193, D.228, W.230, E.254, E.282, H.331, E.351, L.353 Ligands: MG.6 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:W.42, C:P.193, C:L.353 Hydrogen bonds: C:H.35, C:R.61, C:R.61, C:T.175, C:E.282 Water bridges: C:K.191, C:D.228 Salt bridges: C:K.191, C:H.331 3LR.9: 15 residues within 4Å: Chain E: H.35, W.42, I.47, R.61, T.175, K.191, P.193, D.228, W.230, E.254, E.282, H.331, E.351, L.353 Ligands: MG.10 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:W.42, E:P.193, E:L.353 Hydrogen bonds: E:H.35, E:R.61, E:R.61, E:T.175, E:E.282 Water bridges: E:K.191, E:D.228 Salt bridges: E:K.191, E:H.331 3LR.13: 15 residues within 4Å: Chain G: H.35, W.42, I.47, R.61, T.175, K.191, P.193, D.228, W.230, E.254, E.282, H.331, E.351, L.353 Ligands: MG.14 12 PLIP interactions: 12 interactions with chain G Hydrophobic interactions: G:W.42, G:P.193, G:L.353 Hydrogen bonds: G:H.35, G:R.61, G:R.61, G:T.175, G:E.282 Water bridges: G:K.191, G:D.228 Salt bridges: G:K.191, G:H.331

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: K.191, D.228, E.254, E.282 Ligands: 3LR.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.228, A:E.254, A:E.282, H2O.11 MG.3: 5 residues within 4Å: Chain B: K.191, D.228, E.254, E.282 Ligands: 1N5.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.228, B:E.254, B:E.282, H2O.17 MG.6: 5 residues within 4Å: Chain C: K.191, D.228, E.254, E.282 Ligands: 3LR.5 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.228, C:E.254, C:E.282, H2O.27 MG.7: 5 residues within 4Å: Chain D: K.191, D.228, E.254, E.282 Ligands: 1N5.8 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.228, D:E.254, D:E.282, H2O.34 MG.10: 5 residues within 4Å: Chain E: K.191, D.228, E.254, E.282 Ligands: 3LR.9 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.228, E:E.254, E:E.282, H2O.44 MG.11: 5 residues within 4Å: Chain F: K.191, D.228, E.254, E.282 Ligands: 1N5.12 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.228, F:E.254, F:E.282, H2O.51 MG.14: 5 residues within 4Å: Chain G: K.191, D.228, E.254, E.282 Ligands: 3LR.13 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.228, G:E.254, G:E.282, H2O.61 MG.15: 5 residues within 4Å: Chain H: K.191, D.228, E.254, E.282 Ligands: 1N5.16 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.228, H:E.254, H:E.282, H2O.68

4 x 1N5: (2R,4S)-2,4,7-trihydroxyheptanoic acid(Non-covalent)

1N5.4: 14 residues within 4Å: Chain B: H.35, I.47, R.61, T.175, K.191, P.193, D.228, W.230, E.254, E.282, H.331, E.351, L.353 Ligands: MG.3 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.47 Hydrogen bonds: B:R.61, B:R.61, B:D.228, B:D.228, B:E.282 Water bridges: B:H.35, B:K.191, B:W.230 Salt bridges: B:K.191, B:H.331 1N5.8: 14 residues within 4Å: Chain D: H.35, I.47, R.61, T.175, K.191, P.193, D.228, W.230, E.254, E.282, H.331, E.351, L.353 Ligands: MG.7 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:I.47 Hydrogen bonds: D:R.61, D:R.61, D:D.228, D:D.228, D:E.282 Water bridges: D:H.35, D:K.191, D:W.230 Salt bridges: D:K.191, D:H.331 1N5.12: 14 residues within 4Å: Chain F: H.35, I.47, R.61, T.175, K.191, P.193, D.228, W.230, E.254, E.282, H.331, E.351, L.353 Ligands: MG.11 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:I.47 Hydrogen bonds: F:R.61, F:R.61, F:D.228, F:D.228, F:E.282 Water bridges: F:H.35, F:K.191, F:W.230 Salt bridges: F:K.191, F:H.331 1N5.16: 14 residues within 4Å: Chain H: H.35, I.47, R.61, T.175, K.191, P.193, D.228, W.230, E.254, E.282, H.331, E.351, L.353 Ligands: MG.15 12 PLIP interactions: 12 interactions with chain H Hydrophobic interactions: H:I.47 Hydrogen bonds: H:R.61, H:R.61, H:D.228, H:E.282, H:E.282 Water bridges: H:H.35, H:K.191, H:W.230, H:E.254 Salt bridges: H:K.191, H:H.331

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rakus, J.F. et al., Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase. Biochemistry (2008)

Release Date

2008-09-23

Peptides

Putative galactonate dehydratase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

Putative galactonate dehydratase

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