SMTL ID : 3vnk.1

Crystal structures of D-Psicose 3-epimerase with D-fructose from Clostridium cellulolyticum H10

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-tetramer

Ligands

4 x FUD: D-fructose(Non-covalent)

FUD.1: 14 residues within 4Å: Chain A: Y.6, W.14, H.66, W.112, E.150, E.156, D.183, H.186, H.209, R.215, E.244, F.246, I.257 Ligands: MN.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.6, A:E.150, A:E.150, A:E.156, A:R.215, A:R.215, A:E.244 Water bridges: A:H.66, A:G.67 FUD.4: 12 residues within 4Å: Chain B: Y.6, W.14, W.112, E.150, E.156, D.183, H.186, H.209, R.215, E.244, F.246 Ligands: MN.5 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.6, B:E.150, B:E.156, B:R.215, B:R.215, B:E.244 Water bridges: B:Y.6, B:H.66 FUD.7: 13 residues within 4Å: Chain C: Y.6, W.14, G.106, W.112, E.150, E.156, D.183, H.186, H.209, R.215, E.244, F.246 Ligands: MN.8 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:E.150, C:E.156, C:R.215, C:R.215, C:E.244 Water bridges: C:Y.6, C:H.66, C:G.67 FUD.10: 14 residues within 4Å: Chain D: Y.6, W.14, G.67, G.106, W.112, E.150, E.156, D.183, H.186, H.209, R.215, E.244, F.246 Ligands: MN.11 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:E.150, D:E.156, D:R.215, D:R.215, D:E.244 Water bridges: D:Y.6, D:H.66, D:G.67

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

MN.2: 5 residues within 4Å: Chain A: E.150, D.183, H.209, E.244 Ligands: FUD.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.150, A:D.183, A:H.209, A:E.244 MN.3: 2 residues within 4Å: Chain A: K.216, R.220 No protein-ligand interaction detected (PLIP) MN.5: 5 residues within 4Å: Chain B: E.150, D.183, H.209, E.244 Ligands: FUD.4 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.150, B:D.183, B:H.209, B:E.244 MN.6: 3 residues within 4Å: Chain B: D.192 Chain C: R.220 Chain D: E.230 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.192, H2O.18, H2O.22, H2O.32 MN.8: 5 residues within 4Å: Chain C: E.150, D.183, H.209, E.244 Ligands: FUD.7 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.150, C:D.183, C:H.209, C:E.244 MN.9: 2 residues within 4Å: Chain C: K.216, R.220 No protein-ligand interaction detected (PLIP) MN.11: 5 residues within 4Å: Chain D: E.150, D.183, H.209, E.244 Ligands: FUD.10 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.150, D:D.183, D:H.209, D:E.244 MN.12: 3 residues within 4Å: Chain A: R.220 Chain B: E.230 Chain D: D.192 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.192, H2O.13, H2O.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chan, H.C. et al., Crystal structures of D-psicose 3-epimerase from Clostridium cellulolyticum H10 and its complex with ketohexose sugars. Protein Cell (2012)

Release Date

2012-08-01

Peptides

Xylose isomerase domain protein TIM barrel: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Xylose isomerase domain protein TIM barrel

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