SMTL ID : 6oqz.1

Crystal structure of Glucose Isomerase from Non-merohedrally twinned crystals

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 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.6 MN.2: 6 residues within 4Å: Chain A: E.180, E.216, D.244, D.286 Ligands: MG.3, MPD.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.180, A:E.216, A:D.244, A:D.286, H2O.1 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.17 MN.6: 6 residues within 4Å: Chain B: E.180, E.216, D.244, D.286 Ligands: MG.7, MPD.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.180, B:E.216, B:D.244, B:D.286, H2O.12 MN.9: 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.28 MN.10: 6 residues within 4Å: Chain C: E.180, E.216, D.244, D.286 Ligands: MG.11, MPD.12 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.180, C:E.216, C:D.244, C:D.286, H2O.22 MN.13: 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.38 MN.14: 6 residues within 4Å: Chain D: E.180, E.216, D.244, D.286 Ligands: MG.15, MPD.16 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.180, D:E.216, D:D.244, D:D.286, H2O.33

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: E.180, E.216, D.244, D.286 Ligands: MN.2, MPD.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.180, A:E.216, A:D.244, A:D.286, H2O.1 MG.7: 6 residues within 4Å: Chain B: E.180, E.216, D.244, D.286 Ligands: MN.6, MPD.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.180, B:E.216, B:D.244, B:D.286, H2O.12 MG.11: 6 residues within 4Å: Chain C: E.180, E.216, D.244, D.286 Ligands: MN.10, MPD.12 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.180, C:E.216, C:D.244, C:D.286, H2O.22 MG.15: 6 residues within 4Å: Chain D: E.180, E.216, D.244, D.286 Ligands: MN.14, MPD.16 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.180, D:E.216, D:D.244, D:D.286, H2O.33

4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 10 residues within 4Å: Chain A: W.15, H.53, T.89, F.93, V.134, W.136, E.180, D.286 Ligands: MN.2, MG.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.15, A:T.89, A:F.93, A:V.134, A:W.136, A:W.136 Water bridges: A:T.89, A:D.256, A:D.256 MPD.8: 10 residues within 4Å: Chain B: W.15, H.53, T.89, F.93, V.134, W.136, E.180, D.286 Ligands: MN.6, MG.7 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.15, B:T.89, B:F.93, B:V.134, B:W.136, B:W.136 Water bridges: B:T.89, B:D.256, B:D.256 MPD.12: 10 residues within 4Å: Chain C: W.15, H.53, T.89, F.93, V.134, W.136, E.180, D.286 Ligands: MN.10, MG.11 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:W.15, C:T.89, C:F.93, C:V.134, C:W.136, C:W.136 Water bridges: C:D.256, C:D.256 MPD.16: 10 residues within 4Å: Chain D: W.15, H.53, T.89, F.93, V.134, W.136, E.180, D.286 Ligands: MN.14, MG.15 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:W.15, D:T.89, D:F.93, D:V.134, D:W.136, D:W.136 Water bridges: D:D.256, D:D.256, D:D.286

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sevvana, M. et al., Non-merohedral twinning: from minerals to proteins. Acta Crystallogr D Struct Biol (2019)

Release Date

2019-12-11

Peptides

Xylose isomerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Xylose isomerase

Related Entries With Identical Sequence