SMTL ID : 4q7i.2 (1 other biounit)

Crystal structure of engineered thermostable D-tagatose 3-epimerase PcDTE-Var8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: E.152, D.185, H.211, E.246 Ligands: GOL.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.152, A:D.185, A:H.211, A:E.246 MN.4: 3 residues within 4Å: Chain A: H.116 Chain B: H.116 Ligands: IMD.5 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.116, H2O.18 MN.6: 3 residues within 4Å: Chain A: H.98 Chain C: H.98 Ligands: MN.15 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Metal complexes: C:H.98, A:H.98 MN.7: 6 residues within 4Å: Chain B: E.152, D.185, H.211, R.217, E.246 Ligands: GOL.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.152, B:D.185, B:H.211, B:E.246 MN.10: 5 residues within 4Å: Chain C: E.152, D.185, H.211, E.246 Ligands: GOL.11 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.152, C:D.185, C:H.211, C:E.246 MN.13: 3 residues within 4Å: Chain C: H.116 Chain D: H.116 Ligands: IMD.14 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.116, H2O.35 MN.15: 3 residues within 4Å: Chain A: H.98 Chain C: H.98 Ligands: MN.6 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Metal complexes: C:H.98, A:H.98 MN.16: 6 residues within 4Å: Chain D: E.152, D.185, H.211, R.217, E.246 Ligands: GOL.17 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.152, D:D.185, D:H.211, D:E.246

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: W.113, E.152, E.158, D.185, H.188, H.211, R.217, E.246 Ligands: MN.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.158, A:R.217, A:R.217 Water bridges: A:Q.183 GOL.3: 5 residues within 4Å: Chain A: W.15, S.37, I.67, G.68, W.113 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.37, A:S.37, A:G.68 Water bridges: A:I.67 GOL.8: 9 residues within 4Å: Chain B: W.113, E.152, E.158, D.185, H.188, H.211, R.217, E.246 Ligands: MN.7 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.158, B:R.217, B:R.217 Water bridges: B:E.152, B:E.152, B:Q.183 GOL.9: 5 residues within 4Å: Chain B: W.15, S.37, I.67, G.68, W.113 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.37, B:G.68 Water bridges: B:G.68 GOL.11: 9 residues within 4Å: Chain C: W.113, E.152, E.158, D.185, H.188, H.211, R.217, E.246 Ligands: MN.10 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.158, C:R.217, C:R.217 Water bridges: C:Q.183 GOL.12: 5 residues within 4Å: Chain C: W.15, S.37, I.67, G.68, W.113 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.37, C:S.37, C:G.68 Water bridges: C:I.67 GOL.17: 9 residues within 4Å: Chain D: W.113, E.152, E.158, D.185, H.188, H.211, R.217, E.246 Ligands: MN.16 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:E.158, D:R.217, D:R.217 Water bridges: D:E.152, D:E.152, D:Q.183 GOL.18: 5 residues within 4Å: Chain D: W.15, S.37, I.67, G.68, W.113 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.37, D:G.68 Water bridges: D:G.68

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.5: 4 residues within 4Å: Chain A: P.114, H.116 Chain B: H.116 Ligands: MN.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.114 Water bridges: A:H.116 IMD.14: 4 residues within 4Å: Chain C: P.114, H.116 Chain D: H.116 Ligands: MN.13 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:P.114 Water bridges: C:H.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bosshart, A. et al., Directed Divergent Evolution of a Thermostable D-Tagatose Epimerase towards Improved Activity for Two Hexose Substrates. Chembiochem (2015)

Release Date

2014-10-22

Peptides

D-tagatose 3-epimerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

D-tagatose 3-epimerase

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