SMTL ID : 1die.1

OBSERVATIONS OF REACTION INTERMEDIATES AND THE MECHANISM OF ALDOSE-KETOSE INTERCONVERSION BY D-XYLOSE ISOMERASE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: E.216, H.219, N.246, D.254, D.256 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.216, A:H.219, A:D.254, A:D.256, H2O.11 MG.2: 5 residues within 4Å: Chain A: E.180, E.216, D.244, D.292 Ligands: NOJ.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.180, A:E.216, A:D.244, A:D.292 MG.4: 5 residues within 4Å: Chain B: E.216, H.219, N.246, D.254, D.256 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.216, B:H.219, B:D.254, B:D.256, H2O.23 MG.5: 5 residues within 4Å: Chain B: E.180, E.216, D.244, D.292 Ligands: NOJ.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.180, B:E.216, B:D.244, B:D.292 MG.7: 5 residues within 4Å: Chain C: E.216, H.219, N.246, D.254, D.256 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.216, C:H.219, C:D.254, C:D.256, H2O.33 MG.8: 5 residues within 4Å: Chain C: E.180, E.216, D.244, D.292 Ligands: NOJ.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.180, C:E.216, C:D.244, C:D.292 MG.10: 5 residues within 4Å: Chain D: E.216, H.219, N.246, D.254, D.256 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.216, D:H.219, D:D.254, D:D.256, H2O.45 MG.11: 5 residues within 4Å: Chain D: E.180, E.216, D.244, D.292 Ligands: NOJ.12 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.180, D:E.216, D:D.244, D:D.292

4 x NOJ: 1-DEOXYNOJIRIMYCIN(Non-covalent)

NOJ.3: 11 residues within 4Å: Chain A: H.53, T.89, F.93, W.136, E.180, E.216, H.219, D.244, D.292 Chain D: F.25 Ligands: MG.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:H.53, A:T.89, A:E.180 Water bridges: A:W.136, A:N.214, A:E.216, A:H.219, A:D.254, A:D.254 NOJ.6: 10 residues within 4Å: Chain B: H.53, T.89, W.136, E.180, E.216, H.219, D.244, D.292 Chain C: F.25 Ligands: MG.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.53, B:T.89, B:H.219 Water bridges: B:N.214 NOJ.9: 11 residues within 4Å: Chain B: F.25 Chain C: H.53, T.89, F.93, W.136, E.180, E.216, H.219, D.244, D.292 Ligands: MG.8 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:H.53, C:T.89, C:T.89, C:E.180 Water bridges: C:W.136, C:N.214, C:E.216, C:D.254, C:D.254, C:D.254 NOJ.12: 10 residues within 4Å: Chain A: F.25 Chain D: H.53, T.89, W.136, E.180, E.216, H.219, D.244, D.292 Ligands: MG.11 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:H.53, D:T.89, D:T.89, D:H.219, D:D.292 Water bridges: D:N.214

Links

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Citation

Collyer, C.A. et al., Observations of reaction intermediates and the mechanism of aldose-ketose interconversion by D-xylose isomerase. Proc.Natl.Acad.Sci.USA (1990)

Release Date

1993-07-15

Peptides

D-XYLOSE ISOMERASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

D-XYLOSE ISOMERASE

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