SMTL ID : 4gbv.1

Crystal Structure of AMP complexes of Porcine Liver Fructose-1,6-bisphosphatase Mutant A54L with 1,2-ethanediol as Cryo-protectant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

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

F6P.1: 15 residues within 4Å: Chain A: D.121, G.122, N.212, Y.215, Y.244, G.246, S.247, M.248, Y.264, K.274, R.276, E.280 Chain B: R.243 Ligands: PO4.2, MN.4 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.121, A:G.122, A:N.212, A:Y.215, A:Y.244, A:Y.244, A:M.248, A:Y.264, A:K.274, A:R.276 Water bridges: A:S.124, A:Y.215, A:K.274, A:K.274, B:R.243, B:R.243 Salt bridges: A:K.274, B:R.243 F6P.6: 15 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, R.276, E.280 Ligands: PO4.7, MN.9 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.121, B:G.122, B:N.212, B:Y.215, B:Y.244, B:Y.244, B:M.248, B:Y.264, B:K.274, B:R.276 Water bridges: B:S.124, B:Y.215, B:K.274, B:K.274, A:R.243, A:R.243 Salt bridges: B:K.274, A:R.243 F6P.11: 15 residues within 4Å: Chain C: D.121, G.122, N.212, Y.215, Y.244, G.246, S.247, M.248, Y.264, K.274, R.276, E.280 Chain D: R.243 Ligands: PO4.12, MN.14 15 PLIP interactions: 12 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:D.121, C:G.122, C:N.212, C:Y.244, C:M.248, C:K.274, C:R.276 Water bridges: C:S.124, C:Y.215, C:Y.215, C:K.274, D:R.243, D:R.243 Salt bridges: C:K.274, D:R.243 F6P.16: 15 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, R.276, E.280 Ligands: PO4.17, MN.19 15 PLIP interactions: 12 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:D.121, D:G.122, D:N.212, D:Y.244, D:M.248, D:K.274, D:R.276 Water bridges: D:S.124, D:Y.215, D:Y.215, D:K.274, C:R.243, C:R.243 Salt bridges: D:K.274, C:R.243

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

PO4.2: 12 residues within 4Å: Chain A: D.68, E.97, D.118, L.120, D.121, G.122, S.123, R.276, E.280 Ligands: F6P.1, MN.3, MN.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.122, A:S.123, A:S.123, A:E.280 Water bridges: A:N.64, A:S.123 Salt bridges: A:R.276 PO4.7: 12 residues within 4Å: Chain B: D.68, E.97, D.118, L.120, D.121, G.122, S.123, R.276, E.280 Ligands: F6P.6, MN.8, MN.9 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.122, B:S.123, B:S.123, B:E.280 Water bridges: B:N.64, B:S.123 Salt bridges: B:R.276 PO4.12: 12 residues within 4Å: Chain C: D.68, E.97, D.118, L.120, D.121, G.122, S.123, R.276, E.280 Ligands: F6P.11, MN.13, MN.14 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.122, C:S.123, C:S.123, C:E.280, C:E.280 Water bridges: C:N.64, C:S.123 Salt bridges: C:R.276 PO4.17: 12 residues within 4Å: Chain D: D.68, E.97, D.118, L.120, D.121, G.122, S.123, R.276, E.280 Ligands: F6P.16, MN.18, MN.19 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:G.122, D:S.123, D:S.123, D:E.280, D:E.280 Water bridges: D:N.64, D:S.123 Salt bridges: D:R.276

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

MN.3: 6 residues within 4Å: Chain A: E.97, E.98, D.118, P.119, L.120 Ligands: PO4.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.97, A:D.118, A:L.120 MN.4: 7 residues within 4Å: Chain A: E.97, D.118, D.121, G.122, E.280 Ligands: F6P.1, PO4.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.118, A:D.121, A:E.280 MN.8: 6 residues within 4Å: Chain B: E.97, E.98, D.118, P.119, L.120 Ligands: PO4.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.97, B:D.118, B:L.120 MN.9: 7 residues within 4Å: Chain B: E.97, D.118, D.121, G.122, E.280 Ligands: F6P.6, PO4.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.118, B:D.121, B:E.280 MN.13: 6 residues within 4Å: Chain C: E.97, E.98, D.118, P.119, L.120 Ligands: PO4.12 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.97, C:D.118, C:L.120 MN.14: 7 residues within 4Å: Chain C: E.97, D.118, D.121, G.122, E.280 Ligands: F6P.11, PO4.12 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.118, C:D.121, C:E.280 MN.18: 6 residues within 4Å: Chain D: E.97, E.98, D.118, P.119, L.120 Ligands: PO4.17 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.97, D:D.118, D:L.120 MN.19: 7 residues within 4Å: Chain D: E.97, D.118, D.121, G.122, E.280 Ligands: F6P.16, PO4.17 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.5: 14 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, M.177 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:T.27, A:T.27, A:G.28, A:E.29, A:E.29, A:M.30, A:T.31, A:Y.113, A:R.140, A:R.140 Water bridges: A:T.31 Salt bridges: A:K.112 AMP.10: 14 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, K.112, Y.113, R.140, M.177 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:T.27, B:T.27, B:G.28, B:E.29, B:E.29, B:M.30, B:T.31, B:Y.113, B:R.140, B:R.140 Water bridges: B:T.31 Salt bridges: B:K.112 AMP.15: 14 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, M.177 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:T.27, C:T.27, C:T.27, C:G.28, C:E.29, C:M.30, C:T.31, C:T.31, C:Y.113, C:R.140, C:R.140 Water bridges: C:T.31 Salt bridges: C:K.112 AMP.20: 14 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, K.112, Y.113, R.140, M.177 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:T.27, 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, D:R.140 Water bridges: D:T.31 Salt bridges: D:K.112

Links

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Citation

Honzatko, R.B. et al., Water Structure of the Central Hydrophobic Cavity of Mammalian Fructose-1,6-bisphosphatase: a Potential Thermodynamic Determinant of Allowed Quaternary States. To be published

Release Date

2013-08-21

Peptides

Fructose-1,6-bisphosphatase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Fructose-1,6-bisphosphatase 1

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