SMTL ID : 3gnx.1

Structure of dehydrated D-xylose isomerase from streptomyces rubiginosus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x XYL: Xylitol(Non-covalent)

XYL.1: 14 residues within 4Å: Chain A: W.15, H.53, F.93, W.136, E.180, K.182, E.216, H.219, D.244, D.254, D.286 Chain D: F.25 Ligands: MN.2, MN.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.180 Water bridges: A:W.15, A:T.89, A:N.214 XYL.4: 12 residues within 4Å: Chain B: W.15, H.53, F.93, W.136, E.180, E.216, H.219, D.244, D.286 Chain C: F.25 Ligands: MN.5, MN.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.286 Water bridges: B:T.89, B:W.136, B:K.288 XYL.7: 14 residues within 4Å: Chain B: F.25 Chain C: W.15, H.53, F.93, W.136, E.180, K.182, E.216, H.219, D.244, D.254, D.286 Ligands: MN.8, MN.9 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.180 Water bridges: C:W.15, C:T.89, C:N.214 XYL.10: 12 residues within 4Å: Chain A: F.25 Chain D: W.15, H.53, F.93, W.136, E.180, E.216, H.219, D.244, D.286 Ligands: MN.11, MN.12 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.286 Water bridges: D:T.89, D:W.136, D:K.288

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

MN.2: 5 residues within 4Å: Chain A: E.216, N.246, D.256, D.286 Ligands: XYL.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.216, A:D.256 MN.3: 5 residues within 4Å: Chain A: E.180, E.216, D.244, D.286 Ligands: XYL.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.180, A:E.216, A:D.244, A:D.286 MN.5: 6 residues within 4Å: Chain B: W.136, K.182, H.219, D.254 Chain C: F.25 Ligands: XYL.4 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.219, H2O.14 MN.6: 5 residues within 4Å: Chain B: E.180, E.216, D.244, D.286 Ligands: XYL.4 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.180, B:E.216, B:D.244, B:D.286 MN.8: 5 residues within 4Å: Chain C: E.216, N.246, D.256, D.286 Ligands: XYL.7 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.216, C:D.256 MN.9: 5 residues within 4Å: Chain C: E.180, E.216, D.244, D.286 Ligands: XYL.7 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.180, C:E.216, C:D.244, C:D.286 MN.11: 6 residues within 4Å: Chain A: F.25 Chain D: W.136, K.182, H.219, D.254 Ligands: XYL.10 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.219, H2O.31 MN.12: 5 residues within 4Å: Chain D: E.180, E.216, D.244, D.286 Ligands: XYL.10 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.180, D:E.216, D:D.244, D:D.286

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gramiccia, F. et al., Dehydration-induced structural phase transition in crystals of D-xylose isomerase from streptomyces rubiginosus. To be Published

Release Date

2010-03-23

Peptides

Xylose isomerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
A

D
E

Xylose isomerase