SMTL ID : 4zb2.1

A native form of glucose isomerase collected at room temperature.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: E.181, E.217, H.220, D.245, D.287 Ligands: GLC.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.181, A:E.217, A:D.245, A:D.287 MN.2: 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.2 MN.5: 6 residues within 4Å: Chain B: E.181, E.217, H.220, D.245, D.287 Ligands: GLC.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.181, B:E.217, B:D.245, B:D.287 MN.6: 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.14 MN.9: 6 residues within 4Å: Chain C: E.181, E.217, H.220, D.245, D.287 Ligands: GLC.11 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.181, C:E.217, C:D.245, C:D.287 MN.10: 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.25 MN.13: 6 residues within 4Å: Chain D: E.181, E.217, H.220, D.245, D.287 Ligands: GLC.15 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.181, D:E.217, D:D.245, D:D.287 MN.14: 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.37

4 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.3: 13 residues within 4Å: Chain A: W.16, H.54, T.90, F.94, V.135, W.137, E.181, E.217, H.220, D.245, D.287 Chain C: F.26 Ligands: MN.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.90 Water bridges: A:W.16, A:W.137, A:N.215 Salt bridges: A:H.54 GLC.7: 13 residues within 4Å: Chain B: W.16, H.54, T.90, F.94, V.135, W.137, E.181, E.217, H.220, D.245, D.287 Chain D: F.26 Ligands: MN.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.90 Water bridges: B:W.16, B:W.137, B:N.215 Salt bridges: B:H.54 GLC.11: 13 residues within 4Å: Chain A: F.26 Chain C: W.16, H.54, T.90, F.94, V.135, W.137, E.181, E.217, H.220, D.245, D.287 Ligands: MN.9 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.90, C:T.90 Water bridges: C:W.16, C:W.137, C:N.215 Salt bridges: C:H.54 GLC.15: 13 residues within 4Å: Chain B: F.26 Chain D: W.16, H.54, T.90, F.94, V.135, W.137, E.181, E.217, H.220, D.245, D.287 Ligands: MN.13 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.90, D:T.90 Water bridges: D:W.16, D:W.137, D:N.215 Salt bridges: D:H.54

4 x FRU: beta-D-fructofuranose(Non-covalent)

FRU.4: 5 residues within 4Å: Chain A: D.150, R.152, D.153, D.156 Chain D: A.339 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:D.150 Water bridges: A:R.152, A:R.152, A:D.153, A:R.157, D:A.339 FRU.8: 5 residues within 4Å: Chain B: D.150, R.152, D.153, D.156 Chain C: A.339 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:D.150 Water bridges: B:R.152, B:R.152, B:D.153, B:R.157, C:A.339 FRU.12: 5 residues within 4Å: Chain B: A.339 Chain C: D.150, R.152, D.153, D.156 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:D.150, C:R.152 Water bridges: C:R.152, C:R.152, C:D.156, C:R.157, B:A.339 FRU.16: 5 residues within 4Å: Chain A: A.339 Chain D: D.150, R.152, D.153, D.156 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:D.150, D:R.152 Water bridges: D:R.152, D:R.152, D:D.156, D:R.157, A:A.339

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lobley, C.M. et al., A generic protocol for protein crystal dehydration using the HC1b humidity controller. Acta Crystallogr D Struct Biol (2016)

Release Date

2016-03-23

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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