SMTL ID : 3p93.5 (4 other biounits)

Crystal structure of D-mannonate dehydratase from Chromohalobacter Salexigens complexed with MG,D-Mannonate and 2-keto-3-deoxy-D-Gluconate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.213, H.215, E.239, E.265, R.286 Ligands: CS2.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.213, A:E.239, A:E.265, H2O.10 MG.3: 6 residues within 4Å: Chain B: D.213, H.215, E.239, E.265, R.286 Ligands: CS2.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.213, B:E.239, B:E.265, H2O.18 MG.5: 5 residues within 4Å: Chain C: D.213, E.239, E.265, R.286 Ligands: KDG.6 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.213, C:E.239, C:E.265, H2O.18 MG.7: 6 residues within 4Å: Chain D: D.213, H.215, E.239, E.265, R.286 Ligands: KDG.8 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.213, D:E.239, D:E.265, H2O.36 MG.9: 5 residues within 4Å: Chain E: D.213, E.239, E.265, R.286 Ligands: CS2.10 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.213, E:E.239, E:E.265, H2O.45 MG.11: 6 residues within 4Å: Chain F: D.213, H.215, E.239, E.265, R.286 Ligands: CS2.12 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.213, F:E.239, F:E.265, H2O.54 MG.13: 6 residues within 4Å: Chain G: D.213, H.215, E.239, E.265, R.286 Ligands: KDG.14 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.213, G:E.239, G:E.265, H2O.63 MG.15: 5 residues within 4Å: Chain H: D.213, E.239, E.265, R.286 Ligands: KDG.16 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.213, H:E.239, H:E.265, H2O.70

4 x CS2: D-MANNONIC ACID(Non-covalent)

CS2.2: 17 residues within 4Å: Chain A: N.39, H.124, R.149, D.213, H.215, E.239, E.265, R.286, H.315, P.317, D.319, E.342, L.392, W.405 Chain H: Y.77, W.78 Ligands: MG.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.39, A:H.215, A:H.215 Water bridges: A:Y.122, A:R.149, A:R.149, A:E.239 Salt bridges: A:H.124, A:R.149, A:R.286, A:H.315 CS2.4: 17 residues within 4Å: Chain B: N.39, H.124, R.149, D.213, H.215, E.239, E.265, R.286, H.315, P.317, D.319, E.342, L.392, W.405 Chain D: Y.77, W.78 Ligands: MG.3 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:N.39, B:H.215, B:H.215 Water bridges: B:Y.122, B:Y.122, D:Y.77 Salt bridges: B:H.124, B:R.149, B:R.286, B:H.315 CS2.10: 18 residues within 4Å: Chain E: N.39, H.124, R.149, P.173, D.213, H.215, E.239, E.265, R.286, H.315, P.317, D.319, E.342, L.392, W.405 Chain F: Y.77, W.78 Ligands: MG.9 10 PLIP interactions: 9 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:N.39, E:H.215, E:H.215 Water bridges: E:Y.122, E:Y.122, F:Y.77 Salt bridges: E:H.124, E:R.149, E:R.286, E:H.315 CS2.12: 17 residues within 4Å: Chain E: Y.77, W.78 Chain F: N.39, H.124, R.149, D.213, H.215, E.239, E.265, R.286, H.315, P.317, D.319, E.342, L.392, W.405 Ligands: MG.11 12 PLIP interactions: 11 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:N.39, F:D.213, F:H.215, F:H.215, E:Y.77 Water bridges: F:R.149, F:R.149, F:D.319 Salt bridges: F:H.124, F:R.149, F:R.286, F:H.315

4 x KDG: 2-KETO-3-DEOXYGLUCONATE(Non-covalent)

KDG.6: 17 residues within 4Å: Chain C: N.39, H.124, R.149, D.213, H.215, E.239, E.265, R.286, H.315, P.317, D.319, E.342, L.392, W.405 Chain G: Y.77, W.78 Ligands: MG.5 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain G Hydrogen bonds: C:N.39, C:E.265, C:D.319, G:Y.77 Water bridges: C:R.149, C:R.149 Salt bridges: C:H.124, C:R.149, C:R.286, C:H.315 KDG.8: 17 residues within 4Å: Chain B: Y.77, W.78 Chain D: N.39, H.124, R.149, D.213, H.215, E.239, E.265, R.286, H.315, P.317, D.319, E.342, L.392, W.405 Ligands: MG.7 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:N.39, D:E.265, D:D.319, B:Y.77, B:Y.77 Water bridges: D:R.149, D:R.149 Salt bridges: D:H.124, D:R.149, D:R.286, D:H.315 KDG.14: 17 residues within 4Å: Chain C: Y.77, W.78 Chain G: N.39, H.124, R.149, D.213, H.215, E.239, E.265, R.286, H.315, P.317, D.319, E.342, L.392, W.405 Ligands: MG.13 11 PLIP interactions: 9 interactions with chain G, 2 interactions with chain C Hydrogen bonds: G:N.39, G:E.265, G:D.319, C:Y.77 Water bridges: G:Y.122, G:Y.122, C:Y.77 Salt bridges: G:H.124, G:R.149, G:R.286, G:H.315 KDG.16: 17 residues within 4Å: Chain A: Y.77, W.78 Chain H: N.39, H.124, R.149, D.213, H.215, E.239, E.265, R.286, H.315, P.317, D.319, E.342, L.392, W.405 Ligands: MG.15 12 PLIP interactions: 10 interactions with chain H, 2 interactions with chain A Hydrogen bonds: H:N.39, H:D.213, H:E.239, H:D.319, A:Y.77, A:Y.77 Water bridges: H:R.149, H:T.318 Salt bridges: H:H.124, H:R.149, H:R.286, H:H.315

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fedorov, A.A. et al., CRYSTAL STRUCTURE OF D-MANNONATE DEHYDRATASE FROM CHROMOHALOBACTER SALEXIGENS complexed with MG,D-Mannonate and 2-keto-3-deoxy-D-Gluconate. To be Published

Release Date

2011-10-19

Peptides

Mandelate racemase/muconate lactonizing enzyme: 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

Mandelate racemase/muconate lactonizing enzyme

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