SMTL ID : 6quf.1

Protein crystallization by ionic liquid hydrogel support: reference crystal of glucose isomerase grown on standard silanized glass

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.19 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: E.217, H.220, N.247, D.255, D.257 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.217, A:H.220, A:D.255, A:D.257, H2O.12 MN.2: 6 residues within 4Å: Chain A: E.181, E.217, H.220, D.245, D.287 Ligands: GOL.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.181, A:E.217, A:D.245, A:D.287 MN.7: 5 residues within 4Å: Chain B: E.217, H.220, N.247, D.255, D.257 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.217, B:H.220, B:D.255, B:D.257, H2O.33 MN.8: 6 residues within 4Å: Chain B: E.181, E.217, H.220, D.245, D.287 Ligands: GOL.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.181, B:E.217, B:D.245, B:D.287 MN.13: 5 residues within 4Å: Chain C: E.217, H.220, N.247, D.255, D.257 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.217, C:H.220, C:D.255, C:D.257, H2O.53 MN.14: 6 residues within 4Å: Chain C: E.181, E.217, H.220, D.245, D.287 Ligands: GOL.16 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.181, C:E.217, C:D.245, C:D.287 MN.19: 5 residues within 4Å: Chain D: E.217, H.220, N.247, D.255, D.257 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.217, D:H.220, D:D.255, D:D.257, H2O.74 MN.20: 6 residues within 4Å: Chain D: E.181, E.217, H.220, D.245, D.287 Ligands: GOL.22 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.181, D:E.217, D:D.245, D:D.287

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: W.20, D.24, P.25, Y.254, D.255, Q.256, D.257, K.289 Chain C: P.25, P.187 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:D.257 Water bridges: A:D.24, A:E.186, A:K.289, C:P.187 GOL.4: 13 residues within 4Å: Chain A: W.16, H.54, T.90, F.94, V.135, W.137, E.181, N.215, E.217, H.220, D.245, D.287 Ligands: MN.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.54, A:E.181, A:H.220 Water bridges: A:T.90, A:N.215 GOL.6: 5 residues within 4Å: Chain A: G.19, W.20, Q.21, G.22, R.23 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.19, A:W.20, A:Q.21, A:R.23 GOL.9: 10 residues within 4Å: Chain B: W.20, D.24, P.25, Y.254, D.255, Q.256, D.257, K.289 Chain D: P.25, P.187 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:D.257 Water bridges: B:D.24, B:E.186, B:K.289, D:P.187 GOL.10: 13 residues within 4Å: Chain B: W.16, H.54, T.90, F.94, V.135, W.137, E.181, N.215, E.217, H.220, D.245, D.287 Ligands: MN.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.54, B:E.181, B:H.220 Water bridges: B:T.90, B:N.215 GOL.12: 5 residues within 4Å: Chain B: G.19, W.20, Q.21, G.22, R.23 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.19, B:W.20, B:Q.21, B:R.23 GOL.15: 10 residues within 4Å: Chain A: P.25, P.187 Chain C: W.20, D.24, P.25, Y.254, D.255, Q.256, D.257, K.289 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:D.257 Water bridges: C:D.24, C:E.186, C:K.289, A:P.187 GOL.16: 13 residues within 4Å: Chain C: W.16, H.54, T.90, F.94, V.135, W.137, E.181, N.215, E.217, H.220, D.245, D.287 Ligands: MN.14 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.54, C:E.181, C:H.220 Water bridges: C:T.90, C:N.215 GOL.18: 5 residues within 4Å: Chain C: G.19, W.20, Q.21, G.22, R.23 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.19, C:W.20, C:Q.21, C:R.23 GOL.21: 10 residues within 4Å: Chain B: P.25, P.187 Chain D: W.20, D.24, P.25, Y.254, D.255, Q.256, D.257, K.289 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:D.257 Water bridges: D:D.24, D:E.186, D:K.289, B:P.187 GOL.22: 13 residues within 4Å: Chain D: W.16, H.54, T.90, F.94, V.135, W.137, E.181, N.215, E.217, H.220, D.245, D.287 Ligands: MN.20 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:H.54, D:E.181, D:H.220 Water bridges: D:T.90, D:N.215 GOL.24: 5 residues within 4Å: Chain D: G.19, W.20, Q.21, G.22, R.23 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.19, D:W.20, D:Q.21, D:R.23

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 3 residues within 4Å: Chain A: R.23, D.28, A.29 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.29 Water bridges: A:R.23, A:D.28, A:D.28, A:D.28 Salt bridges: A:R.23 SO4.11: 3 residues within 4Å: Chain B: R.23, D.28, A.29 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.29 Water bridges: B:R.23, B:D.28, B:D.28, B:D.28 Salt bridges: B:R.23 SO4.17: 3 residues within 4Å: Chain C: R.23, D.28, A.29 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:A.29 Water bridges: C:R.23, C:R.23, C:R.23, C:R.23 Salt bridges: C:R.23 SO4.23: 3 residues within 4Å: Chain D: R.23, D.28, A.29 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:A.29 Water bridges: D:R.23, D:R.23, D:R.23, D:R.23 Salt bridges: D:R.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Belviso, B.D. et al., Protein Crystallization in Ionic-Liquid Hydrogel Composite Membranes. Crystals (2019)

Release Date

2019-03-13

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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