SMTL ID : 1did.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x DIG: 2,5-DIDEOXY-2,5-IMINO-D-GLUCITOL(Non-covalent)

DIG.1: 13 residues within 4Å: Chain A: W.15, H.53, M.87, F.93, V.134, W.136, E.180, E.216, H.219, D.244, H.290, D.292 Ligands: MN.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.244 Water bridges: A:T.89, A:W.136 DIG.4: 14 residues within 4Å: Chain B: W.15, H.53, M.87, F.93, V.134, W.136, E.180, N.214, E.216, H.219, D.244, H.290, D.292 Ligands: MN.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.244 Water bridges: B:T.89, B:W.136 DIG.7: 13 residues within 4Å: Chain C: W.15, H.53, M.87, F.93, V.134, W.136, E.180, E.216, H.219, D.244, H.290, D.292 Ligands: MN.9 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.244 Water bridges: C:T.89, C:T.89 DIG.10: 14 residues within 4Å: Chain D: W.15, H.53, M.87, F.93, V.134, W.136, E.180, N.214, E.216, H.219, D.244, H.290, D.292 Ligands: MN.12 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.244 Water bridges: D:T.89, D:T.89

8 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 4 residues within 4Å: Chain A: E.216, H.219, 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.4 MN.3: 5 residues within 4Å: Chain A: E.180, E.216, D.244, D.292 Ligands: DIG.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.180, A:E.216, A:D.244, A:D.292 MN.5: 4 residues within 4Å: Chain B: E.216, H.219, 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.15 MN.6: 5 residues within 4Å: Chain B: E.180, E.216, D.244, D.292 Ligands: DIG.4 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.180, B:E.216, B:D.244, B:D.292 MN.8: 4 residues within 4Å: Chain C: E.216, H.219, 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.24 MN.9: 5 residues within 4Å: Chain C: E.180, E.216, D.244, D.292 Ligands: DIG.7 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.180, C:E.216, C:D.244, C:D.292 MN.11: 4 residues within 4Å: Chain D: E.216, H.219, 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.34 MN.12: 5 residues within 4Å: Chain D: E.180, E.216, D.244, D.292 Ligands: DIG.10 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.180, D:E.216, D:D.244, D:D.292

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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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