SMTL ID : 4gws.1

Crystal Structure of AMP complexes of Porcine Liver Fructose-1,6-bisphosphatase with Filled Central Cavity

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-tetramer

Ligands

4 x F6P: 6-O-phosphono-beta-D-fructofuranose(Non-covalent)

F6P.1: 14 residues within 4Å: Chain A: D.121, G.122, N.212, Y.215, Y.244, G.246, M.248, Y.264, K.274, L.275, E.280 Chain B: R.243 Ligands: MG.2, PO4.4 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.122, A:N.212, A:Y.244, A:M.248, A:Y.264, A:K.274, A:E.280 Water bridges: A:S.124, A:S.124 Salt bridges: A:K.274, B:R.243 F6P.5: 14 residues within 4Å: Chain A: R.243 Chain B: D.121, G.122, N.212, Y.215, Y.244, G.246, S.247, M.248, Y.264, K.274, E.280 Ligands: MG.6, PO4.8 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.121, B:G.122, B:S.123, B:N.212, B:Y.215, B:M.248, B:K.274, B:E.280 Water bridges: B:Y.215, B:K.274, B:K.274, A:R.243, A:R.243 Salt bridges: B:K.274, A:R.243 F6P.9: 14 residues within 4Å: Chain C: D.121, G.122, N.212, Y.215, Y.244, G.246, M.248, Y.264, K.274, L.275, E.280 Chain D: R.243 Ligands: MG.10, PO4.12 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.122, C:N.212, C:Y.244, C:M.248, C:Y.264, C:K.274, C:E.280 Water bridges: C:S.124, C:S.124 Salt bridges: C:K.274, D:R.243 F6P.13: 14 residues within 4Å: Chain C: R.243 Chain D: D.121, G.122, N.212, Y.215, Y.244, G.246, S.247, M.248, Y.264, K.274, E.280 Ligands: MG.14, PO4.16 15 PLIP interactions: 12 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:D.121, D:G.122, D:S.123, D:N.212, D:Y.215, D:M.248, D:K.274, D:E.280 Water bridges: D:Y.215, D:K.274, D:K.274, C:R.243, C:R.243 Salt bridges: D:K.274, C:R.243

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.118, D.121, E.280 Ligands: F6P.1, PO4.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.118, A:D.121, A:E.280 MG.6: 6 residues within 4Å: Chain B: E.97, D.118, D.121, E.280 Ligands: F6P.5, PO4.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.118, B:D.121, B:E.280 MG.10: 5 residues within 4Å: Chain C: D.118, D.121, E.280 Ligands: F6P.9, PO4.12 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.118, C:D.121, C:E.280 MG.14: 6 residues within 4Å: Chain D: E.97, D.118, D.121, E.280 Ligands: F6P.13, PO4.16 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.118, D:D.121, D:E.280

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 15 residues within 4Å: Chain A: V.17, E.20, G.21, A.24, G.26, T.27, G.28, E.29, M.30, T.31, K.112, Y.113, R.140, V.160, M.177 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:T.27, A:T.27, A:G.28, A:E.29, A:M.30, A:T.31, A:Y.113, A:Y.113, A:R.140 Water bridges: A:T.31, A:T.31, A:K.112, A:K.112 Salt bridges: A:K.112 AMP.7: 15 residues within 4Å: Chain B: V.17, E.20, G.21, A.24, G.26, T.27, G.28, E.29, M.30, T.31, L.34, K.112, Y.113, R.140, M.177 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:A.24, B:T.27, B:T.27, B:G.28, B:E.29, B:M.30, B:T.31, B:T.31, B:Y.113, B:R.140 Water bridges: B:K.112 Salt bridges: B:K.112 AMP.11: 15 residues within 4Å: Chain C: V.17, E.20, G.21, A.24, G.26, T.27, G.28, E.29, M.30, T.31, K.112, Y.113, R.140, V.160, M.177 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:T.27, C:T.27, C:G.28, C:E.29, C:M.30, C:T.31, C:Y.113, C:Y.113, C:R.140 Water bridges: C:T.31, C:T.31, C:K.112, C:K.112 Salt bridges: C:K.112 AMP.15: 15 residues within 4Å: Chain D: V.17, E.20, G.21, A.24, G.26, T.27, G.28, E.29, M.30, T.31, L.34, K.112, Y.113, R.140, M.177 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:A.24, D:T.27, D:T.27, D:G.28, D:E.29, D:M.30, D:T.31, D:T.31, D:Y.113, D:R.140 Water bridges: D:K.112 Salt bridges: D:K.112

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 9 residues within 4Å: Chain A: E.97, D.118, L.120, D.121, G.122, S.123, E.280 Ligands: F6P.1, MG.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.98, A:L.120, A:G.122, A:S.123, A:S.123 PO4.8: 9 residues within 4Å: Chain B: E.97, D.118, L.120, D.121, G.122, S.123, E.280 Ligands: F6P.5, MG.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:L.120, B:G.122, B:S.123, B:S.123, B:S.123 Water bridges: B:L.120, B:E.280 PO4.12: 9 residues within 4Å: Chain C: E.97, D.118, L.120, D.121, G.122, S.123, E.280 Ligands: F6P.9, MG.10 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.98, C:L.120, C:G.122, C:S.123, C:S.123 PO4.16: 9 residues within 4Å: Chain D: E.97, D.118, L.120, D.121, G.122, S.123, E.280 Ligands: F6P.13, MG.14 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:L.120, D:G.122, D:S.123, D:S.123, D:S.123 Water bridges: D:L.120, D:E.280, D:E.280

Links

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Citation

Gao, Y. et al., Hydrophobic Central Cavity in Fructose-1,6-bisphosphatase is Essential for the Synergism in AMP/Fructose 2,6-bisphosphate Inhibition. To be Published

Release Date

2013-09-04

Peptides

Fructose-1,6-bisphosphatase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Fructose-1,6-bisphosphatase 1

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