SMTL ID : 3roj.1

D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase of Synechocystis sp. PCC 6803

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.131, E.134, E.259 Ligands: CL.16 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.134 MG.2: 5 residues within 4Å: Chain A: D.67, E.91, D.131, P.132, C.133 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.67, H2O.5 MG.22: 4 residues within 4Å: Chain B: D.131, E.134, E.259 Ligands: CL.29 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.131, B:E.134, B:E.259 MG.23: 5 residues within 4Å: Chain B: D.67, E.91, D.131, P.132, C.133 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.67, H2O.12 MG.31: 4 residues within 4Å: Chain C: D.131, E.134, E.259 Ligands: SO4.37 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.131, C:E.134, C:E.259 MG.32: 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.20 MG.45: 4 residues within 4Å: Chain D: D.131, E.134, E.259 Ligands: SO4.49 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.131, D:E.134, D:E.259 MG.46: 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 AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 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 19 PLIP interactions: 10 interactions with chain A, 9 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 Water bridges: A:V.375, A:Q.377, A:Q.377, B:R.198, B:R.198, B:F.243, B:I.248 pi-Stacking: A:F.343, A:F.343 Salt bridges: B:R.198, B:H.249 AMP.21: 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 18 PLIP interactions: 11 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, A:R.198, A:F.243, A:I.248 Salt bridges: A:R.198, A:H.249 pi-Stacking: B:F.343, B:F.343 AMP.33: 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 17 PLIP interactions: 7 interactions with chain D, 10 interactions with chain C Hydrogen bonds: D:R.341, D:R.348, D:V.375, D:Q.377, D:H.379, C:G.245, C:G.245, C:N.247, C:N.247 pi-Stacking: D:F.343, D:F.343 Water bridges: C:R.198, C:S.244, C:T.246, C:I.248 Salt bridges: C:R.198, C:H.249 AMP.34: 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: 6 interactions with chain D, 9 interactions with chain C Hydrogen bonds: D:G.245, D:G.245, D:N.247, C:R.341, C:R.348, C:V.375, C:Q.377, C:H.379 Water bridges: D:R.198, C:Q.377, C:Q.377 Salt bridges: D:R.198, D:H.249 pi-Stacking: C:F.343, C:F.343

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

SO4.4: 4 residues within 4Å: Chain A: Y.165, M.208, R.210, R.212 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain A: R.210, P.211, R.212, V.285 Ligand excluded by PLIP SO4.6: 2 residues within 4Å: Chain A: N.197 Chain B: H.344 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain A: H.344 Chain B: N.197 Ligand excluded by PLIP SO4.8: 1 residues within 4Å: Chain A: K.60 Ligand excluded by PLIP SO4.9: 1 residues within 4Å: Chain A: R.94 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain B: Y.165, M.208, R.210, R.212 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain B: R.210, P.211, R.212, V.285 Ligand excluded by PLIP SO4.35: 4 residues within 4Å: Chain C: Y.165, M.208, R.210, R.212 Ligand excluded by PLIP SO4.36: 4 residues within 4Å: Chain C: R.210, P.211, R.212, V.285 Ligand excluded by PLIP SO4.37: 5 residues within 4Å: Chain C: C.133, E.134, G.135, T.136 Ligands: MG.31 Ligand excluded by PLIP SO4.38: 3 residues within 4Å: Chain C: H.344, K.374 Chain D: N.197 Ligand excluded by PLIP SO4.47: 4 residues within 4Å: Chain D: Y.165, M.208, R.210, R.212 Ligand excluded by PLIP SO4.48: 4 residues within 4Å: Chain D: R.210, P.211, R.212, V.285 Ligand excluded by PLIP SO4.49: 6 residues within 4Å: Chain D: C.133, E.134, G.135, T.136, N.137 Ligands: MG.45 Ligand excluded by PLIP SO4.50: 3 residues within 4Å: Chain C: N.197 Chain D: H.344, K.374 Ligand excluded by PLIP SO4.51: 4 residues within 4Å: Chain D: D.163, F.164, Y.165, A.256 Ligand excluded by PLIP

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

CL.10: 5 residues within 4Å: Chain A: R.268, A.319, C.320, G.321, V.324 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain A: E.105 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: N.144, G.334, T.335 Chain B: N.144 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: D.234, A.256 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: R.212, E.215 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain A: Q.143 Ligand excluded by PLIP CL.16: 6 residues within 4Å: Chain A: C.133, E.134, G.135, T.136, D.232 Ligands: MG.1 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain A: R.86 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain A: Q.275, V.312, Y.313, N.314 Ligands: GOL.20 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain A: N.79, G.107 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain B: Y.101, E.104, E.105 Ligand excluded by PLIP CL.27: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain B: P.211, R.212 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain B: G.135, T.136 Ligands: MG.22 Ligand excluded by PLIP CL.30: 1 residues within 4Å: Chain B: C.269 Ligand excluded by PLIP CL.39: 2 residues within 4Å: Chain C: S.358, T.360 Ligand excluded by PLIP CL.40: 3 residues within 4Å: Chain C: R.268, C.269, G.271 Ligand excluded by PLIP CL.41: 4 residues within 4Å: Chain C: K.176, H.273, F.274, C.315 Ligand excluded by PLIP CL.42: 2 residues within 4Å: Chain C: N.79, R.111 Ligand excluded by PLIP CL.43: 2 residues within 4Å: Chain C: D.163, Y.165 Ligand excluded by PLIP CL.44: 2 residues within 4Å: Chain C: Q.143, N.144 Ligand excluded by PLIP CL.52: 3 residues within 4Å: Chain A: C.269 Chain D: E.371, S.372 Ligand excluded by PLIP CL.53: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.20: 10 residues within 4Å: Chain A: K.176, G.177, G.272, H.273, F.274, Q.275, N.314, C.315, E.316 Ligands: CL.18 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.272, A:F.274, A:C.315 Water bridges: A:G.177, A:Q.275, A:N.314, A:E.316, A:E.316

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

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