SMTL ID : 3ctl.1 (3 other biounits)

Crystal structure of D-Allulose 6-Phosphate 3-Epimerase from Escherichia coli K12 complexed with D-glucitol 6-phosphate and magnesium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

6 x S6P: D-SORBITOL-6-PHOSPHATE(Non-covalent)

S6P.1: 20 residues within 4Å: Chain A: S.6, M.8, H.30, D.32, H.63, M.65, M.135, P.139, G.140, F.141, A.142, G.143, D.173, G.174, S.175, G.195, T.196, S.197, G.198 Ligands: MG.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.6, A:H.30, A:D.32, A:G.140, A:G.143, A:D.173, A:S.175, A:T.196, A:T.196, A:S.197, A:G.198 Water bridges: A:G.174, A:C.176, A:G.195, A:G.195 S6P.3: 21 residues within 4Å: Chain B: S.6, M.8, C.9, H.30, D.32, H.63, M.65, M.135, P.139, G.140, F.141, A.142, G.143, D.173, G.174, S.175, G.195, T.196, S.197, G.198 Ligands: MG.4 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:S.6, B:D.32, B:H.63, B:G.140, B:G.143, B:D.173, B:D.173, B:G.174, B:S.175, B:T.196, B:S.197, B:G.198 Water bridges: B:Q.144, B:Q.144, B:C.176, B:C.176, B:G.195 S6P.5: 20 residues within 4Å: Chain C: S.6, M.8, H.30, D.32, H.63, M.65, M.135, P.139, G.140, F.141, A.142, G.143, D.173, G.174, S.175, G.195, T.196, S.197, G.198 Ligands: MG.6 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:S.6, C:H.30, C:D.32, C:G.140, C:G.143, C:D.173, C:S.175, C:T.196, C:S.197, C:G.198 Water bridges: C:D.173, C:D.173, C:C.176, C:G.195 S6P.7: 21 residues within 4Å: Chain D: S.6, M.8, C.9, H.30, D.32, H.63, M.65, M.135, P.139, G.140, F.141, A.142, G.143, D.173, G.174, S.175, G.195, T.196, S.197, G.198 Ligands: MG.8 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:S.6, D:H.30, D:D.32, D:H.63, D:G.140, D:G.143, D:D.173, D:S.175, D:T.196, D:S.197, D:G.198 Water bridges: D:D.173, D:G.174, D:C.176 S6P.9: 21 residues within 4Å: Chain E: S.6, M.8, C.9, H.30, D.32, H.63, M.65, M.135, P.139, G.140, F.141, A.142, G.143, D.173, G.174, S.175, G.195, T.196, S.197, G.198 Ligands: MG.10 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:S.6, E:D.32, E:G.140, E:G.143, E:D.173, E:D.173, E:S.175, E:T.196, E:T.196, E:S.197, E:G.198 Water bridges: E:G.174, E:G.174, E:C.176, E:G.195 S6P.11: 21 residues within 4Å: Chain F: S.6, M.8, C.9, H.30, D.32, H.63, M.65, M.135, P.139, G.140, F.141, A.142, G.143, D.173, G.174, S.175, G.195, T.196, S.197, G.198 Ligands: MG.12 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:S.6, F:H.30, F:D.32, F:H.63, F:G.140, F:G.143, F:D.173, F:S.175, F:T.196, F:T.196, F:S.197, F:G.198 Water bridges: F:Q.144, F:G.174, F:C.176, F:C.176

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: H.30, D.32, H.63, M.65, D.173 Ligands: S6P.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.30, A:D.32, A:H.63, A:D.173 MG.4: 5 residues within 4Å: Chain B: H.30, D.32, H.63, D.173 Ligands: S6P.3 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.30, B:D.32, B:H.63, B:D.173 MG.6: 6 residues within 4Å: Chain C: H.30, D.32, H.63, M.65, D.173 Ligands: S6P.5 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.30, C:D.32, C:H.63, C:D.173 MG.8: 5 residues within 4Å: Chain D: H.30, D.32, H.63, D.173 Ligands: S6P.7 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.30, D:D.32, D:H.63, D:D.173 MG.10: 6 residues within 4Å: Chain E: H.30, D.32, H.63, M.65, D.173 Ligands: S6P.9 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.30, E:D.32, E:H.63, E:D.173 MG.12: 6 residues within 4Å: Chain F: H.30, D.32, H.63, M.65, D.173 Ligands: S6P.11 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.30, F:D.32, F:H.63, F:D.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chan, K.K. et al., Structural basis for substrate specificity in phosphate binding (beta/alpha)8-barrels: D-allulose 6-phosphate 3-epimerase from Escherichia coli K-12. Biochemistry (2008)

Release Date

2009-02-24

Peptides

D-allulose-6-phosphate 3-epimerase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

D-allulose-6-phosphate 3-epimerase

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