SMTL ID : 3rpl.1

D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase of Synechocystis sp. PCC 6803 in complex with FRUCTOSE-1,6-BISPHOSPHATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.232 Ligands: FBP.4 No protein-ligand interaction detected (PLIP) MG.2: 4 residues within 4Å: Chain A: D.131, E.134, E.259 Ligands: FBP.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.131, A:E.134, A:E.259, H2O.3 MG.3: 5 residues within 4Å: Chain A: D.67, E.91, D.131, P.132, C.133 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.67 MG.11: 3 residues within 4Å: Chain B: R.210, D.232 Ligands: FBP.14 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.232 MG.12: 5 residues within 4Å: Chain B: D.131, E.134, G.135, E.259 Ligands: FBP.14 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.131, B:E.259, H2O.9 MG.13: 5 residues within 4Å: Chain B: D.67, E.91, D.131, P.132, C.133 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.67 MG.18: 2 residues within 4Å: Chain C: D.232 Ligands: FBP.21 No protein-ligand interaction detected (PLIP) MG.19: 4 residues within 4Å: Chain C: D.131, E.134, E.259 Ligands: FBP.21 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.131, C:E.134, C:E.259 MG.20: 5 residues within 4Å: Chain C: D.67, E.91, D.131, P.132, C.133 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.67, C:E.91, H2O.17 MG.32: 2 residues within 4Å: Chain D: D.232 Ligands: FBP.35 No protein-ligand interaction detected (PLIP) MG.33: 4 residues within 4Å: Chain D: D.131, E.134, E.259 Ligands: FBP.35 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.131, D:E.259, H2O.27 MG.34: 5 residues within 4Å: Chain D: D.67, E.91, D.131, P.132, C.133 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.67

4 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)

FBP.4: 18 residues within 4Å: Chain A: C.133, E.134, G.135, T.136, N.137, Y.165, K.168, M.208, R.210, R.212, D.232, G.233, D.234, G.255, A.256, E.259 Ligands: MG.1, MG.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:E.134, A:G.135, A:T.136, A:T.136, A:N.137, A:Y.165, A:Y.165, A:K.168, A:D.232, A:D.232, A:G.233, A:D.234, A:D.234, A:A.256 Water bridges: A:R.210 Salt bridges: A:R.210, A:R.212 FBP.14: 16 residues within 4Å: Chain B: C.133, E.134, G.135, T.136, Y.165, M.208, R.210, R.212, D.232, G.233, D.234, G.255, A.256, E.259 Ligands: MG.11, MG.12 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:E.134, B:G.135, B:T.136, B:T.136, B:N.137, B:K.168, B:G.233, B:D.234, B:D.234, B:D.234, B:A.256 Water bridges: B:T.136 Salt bridges: B:R.210, B:R.212 FBP.21: 17 residues within 4Å: Chain C: C.133, E.134, G.135, T.136, Y.165, K.168, M.208, R.210, R.212, D.232, G.233, D.234, G.255, A.256, E.259 Ligands: MG.18, MG.19 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:E.134, C:G.135, C:T.136, C:T.136, C:T.136, C:K.168, C:D.232, C:G.233, C:D.234, C:D.234, C:A.256 Water bridges: C:N.137, C:N.137 Salt bridges: C:R.210, C:R.212 FBP.35: 18 residues within 4Å: Chain D: C.133, E.134, G.135, T.136, N.137, Y.165, K.168, M.208, R.210, R.212, D.232, G.233, D.234, G.255, A.256, E.259 Ligands: MG.32, MG.33 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:E.134, D:G.135, D:T.136, D:T.136, D:N.137, D:Y.165, D:G.233, D:D.234, D:D.234, D:D.234, D:A.256 Salt bridges: D:R.210, D:R.212

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.5: 13 residues within 4Å: Chain A: R.341, F.343, R.348, V.375, I.376, Q.377, H.379 Chain B: R.198, S.244, G.245, T.246, N.247, H.249 17 PLIP interactions: 7 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:R.341, A:R.348, A:V.375, A:Q.377, A:H.379, B:G.245, B:G.245, B:N.247, B:N.247 pi-Stacking: A:F.343, A:F.343 Water bridges: B:R.198, B:R.198, B:F.243, B:I.248 Salt bridges: B:R.198, B:H.249 AMP.10: 13 residues within 4Å: Chain A: R.198, S.244, G.245, T.246, N.247, H.249 Chain B: R.341, F.343, R.348, V.375, I.376, Q.377, H.379 15 PLIP interactions: 8 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:G.245, A:G.245, A:N.247, A:N.247, B:R.341, B:R.348, B:V.375, B:Q.377, B:H.379 Water bridges: A:R.198, A:R.198 Salt bridges: A:R.198, A:H.249 pi-Stacking: B:F.343, B:F.343 AMP.22: 13 residues within 4Å: Chain C: R.341, F.343, R.348, V.375, I.376, Q.377, H.379 Chain D: R.198, S.244, G.245, T.246, N.247, H.249 15 PLIP interactions: 8 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:G.245, D:G.245, D:N.247, D:N.247, C:R.341, C:R.348, C:V.375, C:Q.377, C:H.379 Water bridges: D:R.198, D:R.198 Salt bridges: D:R.198, D:H.249 pi-Stacking: C:F.343, C:F.343 AMP.31: 13 residues within 4Å: Chain C: R.198, S.244, G.245, T.246, N.247, H.249 Chain D: R.341, F.343, R.348, V.375, I.376, Q.377, H.379 15 PLIP interactions: 8 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:G.245, C:G.245, C:N.247, C:N.247, D:R.341, D:R.348, D:V.375, D:Q.377, D:H.379 Water bridges: C:T.246, C:I.248 Salt bridges: C:R.198, C:H.249 pi-Stacking: D:F.343, D:F.343

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

SO4.6: 4 residues within 4Å: Chain A: R.210, P.211, R.212, V.285 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.212 Salt bridges: A:R.212 SO4.7: 2 residues within 4Å: Chain A: H.344 Chain B: N.197 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:H.344 Hydrogen bonds: B:N.197 SO4.8: 4 residues within 4Å: Chain A: N.79, G.107, T.110, R.111 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.110, A:T.110 Water bridges: A:N.79 Salt bridges: A:R.111 SO4.15: 4 residues within 4Å: Chain B: R.210, P.211, R.212, V.285 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.212 Water bridges: B:K.286 Salt bridges: B:R.212 SO4.16: 2 residues within 4Å: Chain A: N.197 Chain B: H.344 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:H.344 Hydrogen bonds: A:N.197, A:N.197 SO4.17: 1 residues within 4Å: Chain B: R.94 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.94 SO4.23: 4 residues within 4Å: Chain C: R.210, P.211, R.212, V.285 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.212 Salt bridges: C:R.212 SO4.24: 3 residues within 4Å: Chain C: H.344, K.374 Chain D: N.197 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Water bridges: C:K.374 Salt bridges: C:H.344 Hydrogen bonds: D:N.197 SO4.25: 4 residues within 4Å: Chain C: E.62, K.63, N.64, T.65 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.63, C:N.64, C:N.64, C:T.65 SO4.36: 4 residues within 4Å: Chain D: R.210, P.211, R.212, V.285 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.212, D:V.284 Salt bridges: D:R.212 SO4.37: 2 residues within 4Å: Chain C: N.197 Chain D: H.344 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:N.197 Salt bridges: D:H.344

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 1 residues within 4Å: Chain A: R.94 Ligand excluded by PLIP CL.26: 5 residues within 4Å: Chain C: K.176, H.273, F.274, N.314, C.315 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain C: I.254 Ligands: GOL.30 Ligand excluded by PLIP CL.28: 1 residues within 4Å: Chain B: S.244 Ligand excluded by PLIP CL.29: 1 residues within 4Å: Chain C: D.163 Ligand excluded by PLIP CL.38: 4 residues within 4Å: Chain D: L.138, Q.143, S.231, D.232 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.30: 10 residues within 4Å: Chain C: K.167, K.168, K.183, S.184, A.185, N.188, L.216, M.252, G.253 Ligands: CL.27 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:K.168, C:S.184, C:N.188, C:G.253 Water bridges: C:K.167, C:K.167

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, X. et al., New insights into the structural and interactional basis for a promising route towards fructose-1,6-/sedoheptulose-1,7-bisphosphatases controlling. To be Published

Release Date

2012-05-02

Peptides

D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase

Related Entries With Identical Sequence