SMTL ID : 7dmm.1

Structure of a glucose isomerase crystal grown in an aqueous glycerol solution without any precipitants

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.99 Å

Oligo State

homo-tetramer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: H.53, F.93, W.136, E.180, E.216, H.219, D.244, D.286 Ligands: MN.5 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.89, A:T.90, A:N.214 GOL.2: 4 residues within 4Å: Chain A: Y.253, D.254, Q.255 Chain C: P.24 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.255 Water bridges: A:D.23, A:Y.253, C:P.186 GOL.6: 9 residues within 4Å: Chain B: H.53, F.93, W.136, E.180, E.216, H.219, D.244, D.286 Ligands: MN.10 3 PLIP interactions: 3 interactions with chain B Water bridges: B:T.89, B:T.90, B:N.214 GOL.7: 4 residues within 4Å: Chain B: Y.253, D.254, Q.255 Chain D: P.24 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B Water bridges: D:P.186, B:D.23, B:Y.253 Hydrogen bonds: B:Q.255 GOL.11: 9 residues within 4Å: Chain C: H.53, F.93, W.136, E.180, E.216, H.219, D.244, D.286 Ligands: MN.15 3 PLIP interactions: 3 interactions with chain C Water bridges: C:T.89, C:T.90, C:N.214 GOL.12: 4 residues within 4Å: Chain A: P.24 Chain C: Y.253, D.254, Q.255 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.255 Water bridges: C:Y.253, A:P.186 GOL.16: 9 residues within 4Å: Chain D: H.53, F.93, W.136, E.180, E.216, H.219, D.244, D.286 Ligands: MN.20 3 PLIP interactions: 3 interactions with chain D Water bridges: D:T.89, D:T.90, D:N.214 GOL.17: 4 residues within 4Å: Chain B: P.24 Chain D: Y.253, D.254, Q.255 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:Q.255 Water bridges: D:Y.253, B:P.186

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: G.260, A.261, G.262, L.264 Chain B: R.265, M.379 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:G.260, A:G.262 CA.8: 6 residues within 4Å: Chain A: R.265, M.379 Chain B: G.260, A.261, G.262, L.264 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:G.260, B:G.262 CA.13: 6 residues within 4Å: Chain C: G.260, A.261, G.262, L.264 Chain D: R.265, M.379 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:G.260, C:G.262 CA.18: 6 residues within 4Å: Chain C: R.265, M.379 Chain D: G.260, A.261, G.262, L.264 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:G.260, D:G.262

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

MN.4: 5 residues within 4Å: Chain A: E.216, H.219, N.246, 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.1 MN.5: 5 residues within 4Å: Chain A: E.180, E.216, D.244, D.286 Ligands: GOL.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.180, A:E.216, A:D.244, A:D.286 MN.9: 5 residues within 4Å: Chain B: E.216, H.219, N.246, 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.13 MN.10: 5 residues within 4Å: Chain B: E.180, E.216, D.244, D.286 Ligands: GOL.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.180, B:E.216, B:D.244, B:D.286 MN.14: 5 residues within 4Å: Chain C: E.216, H.219, N.246, 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.25 MN.15: 5 residues within 4Å: Chain C: E.180, E.216, D.244, D.286 Ligands: GOL.11 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.180, C:E.216, C:D.244, C:D.286 MN.19: 5 residues within 4Å: Chain D: E.216, H.219, N.246, 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.36 MN.20: 5 residues within 4Å: Chain D: E.180, E.216, D.244, D.286 Ligands: GOL.16 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

Suzuki, Y. et al., Extraordinarily fast growth of high-quality glucose isomerase crystals simply by concentration in a precipitant-free solution with a cryoprotectant. To be published

Release Date

2021-12-08

Peptides

Xylose isomerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Xylose isomerase