SMTL ID : 8wdg.1

Subatomic crystal structure of glucose isomerase from Streptomyces rubiginosus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.99 Å

Oligo State

homo-tetramer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 7 residues within 4Å: Chain A: K.181, E.215, H.218, N.245, D.253, D.255 Ligands: XYL.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.215, A:H.218, A:D.253, A:D.255, H2O.2 MG.2: 6 residues within 4Å: Chain A: E.179, E.215, H.218, D.243, D.285 Ligands: XYL.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.179, A:E.215, A:D.243, A:D.285 MG.4: 7 residues within 4Å: Chain A: V.216, Q.220, G.246, Q.247, A.260, G.261, D.262 No protein-ligand interaction detected (PLIP) MG.5: 7 residues within 4Å: Chain B: K.181, E.215, H.218, N.245, D.253, D.255 Ligands: XYL.7 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.215, B:H.218, B:D.253, B:D.255, H2O.22 MG.6: 6 residues within 4Å: Chain B: E.179, E.215, H.218, D.243, D.285 Ligands: XYL.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.179, B:E.215, B:D.243, B:D.285 MG.8: 7 residues within 4Å: Chain B: V.216, Q.220, G.246, Q.247, A.260, G.261, D.262 No protein-ligand interaction detected (PLIP) MG.9: 7 residues within 4Å: Chain C: K.181, E.215, H.218, N.245, D.253, D.255 Ligands: XYL.11 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.215, C:H.218, C:D.253, C:D.255, H2O.41 MG.10: 6 residues within 4Å: Chain C: E.179, E.215, H.218, D.243, D.285 Ligands: XYL.11 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.179, C:E.215, C:D.243, C:D.285 MG.12: 7 residues within 4Å: Chain C: V.216, Q.220, G.246, Q.247, A.260, G.261, D.262 No protein-ligand interaction detected (PLIP) MG.13: 7 residues within 4Å: Chain D: K.181, E.215, H.218, N.245, D.253, D.255 Ligands: XYL.15 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.215, D:H.218, D:D.253, D:D.255, H2O.60 MG.14: 6 residues within 4Å: Chain D: E.179, E.215, H.218, D.243, D.285 Ligands: XYL.15 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.179, D:E.215, D:D.243, D:D.285 MG.16: 7 residues within 4Å: Chain D: V.216, Q.220, G.246, Q.247, A.260, G.261, D.262 No protein-ligand interaction detected (PLIP)

4 x XYL: Xylitol(Non-covalent)

XYL.3: 16 residues within 4Å: Chain A: W.14, H.52, T.88, F.92, V.133, W.135, E.179, K.181, E.215, H.218, D.243, D.253, D.285 Chain C: F.24 Ligands: MG.1, MG.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:W.14, A:H.52, A:K.181, A:E.215, A:H.218, A:D.285 Water bridges: A:T.88, A:T.89, A:N.213 XYL.7: 16 residues within 4Å: Chain B: W.14, H.52, T.88, F.92, V.133, W.135, E.179, K.181, E.215, H.218, D.243, D.253, D.285 Chain D: F.24 Ligands: MG.5, MG.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:W.14, B:H.52, B:K.181, B:E.215, B:H.218, B:D.285 Water bridges: B:T.88, B:T.89, B:N.213 XYL.11: 16 residues within 4Å: Chain A: F.24 Chain C: W.14, H.52, T.88, F.92, V.133, W.135, E.179, K.181, E.215, H.218, D.243, D.253, D.285 Ligands: MG.9, MG.10 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:W.14, C:H.52, C:K.181, C:E.215, C:H.218, C:D.285 Water bridges: C:T.88, C:T.89, C:N.213 XYL.15: 16 residues within 4Å: Chain B: F.24 Chain D: W.14, H.52, T.88, F.92, V.133, W.135, E.179, K.181, E.215, H.218, D.243, D.253, D.285 Ligands: MG.13, MG.14 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:W.14, D:H.52, D:K.181, D:E.215, D:H.218, D:D.285 Water bridges: D:T.88, D:T.89, D:N.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Y. et al., Xylitol binding to the M1 site of glucose isomerase induces a conformational change in the substrate binding channel. Biochem.Biophys.Res.Commun. (2023)

Release Date

2023-10-04

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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