SMTL ID : 4duo.1

Room-temperature X-ray structure of D-Xylose Isomerase in complex with 2Mg2+ ions and xylitol at pH 7.7

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: E.217, H.220, D.255, D.257 Ligands: XYL.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.217, A:H.220, A:D.257, H2O.1 MG.2: 5 residues within 4Å: Chain A: E.181, E.217, D.245, D.287 Ligands: XYL.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.181, A:E.217, A:D.245, A:D.287 MG.4: 5 residues within 4Å: Chain B: E.217, H.220, D.255, D.257 Ligands: XYL.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.217, B:H.220, B:D.257, H2O.9 MG.5: 5 residues within 4Å: Chain B: E.181, E.217, D.245, D.287 Ligands: XYL.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.181, B:E.217, B:D.245, B:D.287 MG.7: 5 residues within 4Å: Chain C: E.217, H.220, D.255, D.257 Ligands: XYL.9 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.217, C:H.220, C:D.257, H2O.18 MG.8: 5 residues within 4Å: Chain C: E.181, E.217, D.245, D.287 Ligands: XYL.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.181, C:E.217, C:D.245, C:D.287 MG.10: 5 residues within 4Å: Chain D: E.217, H.220, D.255, D.257 Ligands: XYL.12 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.217, D:H.220, D:D.257, H2O.27 MG.11: 5 residues within 4Å: Chain D: E.181, E.217, D.245, D.287 Ligands: XYL.12 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.181, D:E.217, D:D.245, D:D.287

4 x XYL: Xylitol(Non-covalent)

XYL.3: 14 residues within 4Å: Chain A: W.16, H.54, F.94, W.137, E.181, K.183, E.217, H.220, D.245, D.255, D.287 Chain C: F.26 Ligands: MG.1, MG.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:H.54, A:E.181, A:H.220, A:D.255, A:D.255 Water bridges: A:W.16, A:N.215, A:D.287, A:D.287 XYL.6: 14 residues within 4Å: Chain B: W.16, H.54, F.94, W.137, E.181, K.183, E.217, H.220, D.245, D.255, D.287 Chain D: F.26 Ligands: MG.4, MG.5 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:H.54, B:E.181, B:H.220, B:D.255, B:D.255 Water bridges: B:W.16, B:N.215, B:D.287, B:D.287 XYL.9: 14 residues within 4Å: Chain A: F.26 Chain C: W.16, H.54, F.94, W.137, E.181, K.183, E.217, H.220, D.245, D.255, D.287 Ligands: MG.7, MG.8 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:H.54, C:E.181, C:H.220, C:D.255 Water bridges: C:W.16, C:T.90, C:D.287, C:D.287, C:D.287 XYL.12: 14 residues within 4Å: Chain B: F.26 Chain D: W.16, H.54, F.94, W.137, E.181, K.183, E.217, H.220, D.245, D.255, D.287 Ligands: MG.10, MG.11 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:H.54, D:E.181, D:H.220, D:D.255 Water bridges: D:W.16, D:T.90, D:D.287, D:D.287, D:D.287

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kovalevsky, A. et al., Inhibition of D-xylose isomerase by polyols: atomic details by joint X-ray/neutron crystallography. Acta Crystallogr.,Sect.D (2012)

Release Date

2012-08-29

Peptides

Xylose isomerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Xylose isomerase

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