SMTL ID : 4gbw.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

F6P.1: 16 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, L.275, R.276, E.280 Chain B: R.243 Ligands: MN.4, PO4.5 21 PLIP interactions: 18 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, A:E.280 Water bridges: A:S.124, A:S.124, A:S.124, A:S.124, A:Y.215, A:Y.264, B:R.243, B:R.243 Salt bridges: A:K.274, B:R.243 F6P.7: 16 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, L.275, R.276, E.280 Ligands: MN.10, PO4.11 21 PLIP interactions: 18 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, B:E.280 Water bridges: B:S.124, B:S.124, B:S.124, B:S.124, B:Y.215, B:Y.264, A:R.243, A:R.243 Salt bridges: B:K.274, A:R.243 F6P.13: 16 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, L.275, R.276, E.280 Chain D: R.243 Ligands: MN.16, PO4.17 18 PLIP interactions: 15 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, C:E.280 Water bridges: C:S.124, C:S.124, C:S.124, C:S.124, C:Y.215, C:Y.264, D:R.243, D:R.243 Salt bridges: C:K.274, D:R.243 F6P.19: 16 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, L.275, R.276, E.280 Ligands: MN.22, PO4.23 18 PLIP interactions: 15 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, D:E.280 Water bridges: D:S.124, D:S.124, D:S.124, D:S.124, D:Y.215, D:Y.264, C:R.243, C:R.243 Salt bridges: D:K.274, C:R.243

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

MN.2: 6 residues within 4Å: Chain A: E.97, D.118, L.120, D.121 Ligands: MN.3, PO4.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.97, A:D.118, A:L.120 MN.3: 6 residues within 4Å: Chain A: N.64, D.68, E.97, R.276 Ligands: MN.2, PO4.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.68, A:E.97 MN.4: 6 residues within 4Å: Chain A: D.118, D.121, G.122, E.280 Ligands: F6P.1, PO4.5 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, D.118, L.120, D.121 Ligands: MN.9, PO4.11 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.97, B:D.118, B:L.120 MN.9: 6 residues within 4Å: Chain B: N.64, D.68, E.97, R.276 Ligands: MN.8, PO4.11 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.68, B:E.97 MN.10: 6 residues within 4Å: Chain B: D.118, D.121, G.122, E.280 Ligands: F6P.7, PO4.11 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.118, B:D.121, B:E.280 MN.14: 6 residues within 4Å: Chain C: E.97, D.118, L.120, D.121 Ligands: MN.15, PO4.17 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.97, C:D.118, C:L.120 MN.15: 6 residues within 4Å: Chain C: N.64, D.68, E.97, R.276 Ligands: MN.14, PO4.17 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.68, C:E.97 MN.16: 6 residues within 4Å: Chain C: D.118, D.121, G.122, E.280 Ligands: F6P.13, PO4.17 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.118, C:D.121, C:E.280 MN.20: 6 residues within 4Å: Chain D: E.97, D.118, L.120, D.121 Ligands: MN.21, PO4.23 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.97, D:D.118, D:L.120 MN.21: 6 residues within 4Å: Chain D: N.64, D.68, E.97, R.276 Ligands: MN.20, PO4.23 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.68, D:E.97 MN.22: 6 residues within 4Å: Chain D: D.118, D.121, G.122, E.280 Ligands: F6P.19, PO4.23 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.118, D:D.121, D:E.280

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

PO4.5: 13 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.2, MN.3, MN.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.122, A:S.123, A:S.123 Salt bridges: A:R.276 PO4.11: 13 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.7, MN.8, MN.9, MN.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.122, B:S.123, B:S.123 Salt bridges: B:R.276 PO4.17: 13 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.13, MN.14, MN.15, MN.16 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.97, C:G.122, C:S.123, C:S.123, C:E.280 Salt bridges: C:R.276 PO4.23: 13 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.19, MN.20, MN.21, MN.22 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.122, D:S.123, D:S.123, D:E.280 Salt bridges: D:R.276

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.6: 16 residues within 4Å: Chain A: V.17, M.18, 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:V.17, A:G.21, A:T.27, A:T.27, A:T.27, A:G.28, A:E.29, A:M.30, A:Y.113, A:R.140, A:R.140 Water bridges: A:T.31, A:T.31 Salt bridges: A:K.112 AMP.12: 16 residues within 4Å: Chain B: V.17, M.18, 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 B Hydrogen bonds: B:V.17, B:G.21, B:T.27, B:T.27, B:T.27, B:G.28, B:E.29, B:M.30, B:Y.113, B:R.140, B:R.140 Water bridges: B:T.31, B:T.31 Salt bridges: B:K.112 AMP.18: 16 residues within 4Å: Chain C: V.17, M.18, 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 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:V.17, C:G.21, C:T.27, C:T.27, C:T.27, C:G.28, C:E.29, C:M.30, C:T.31, C:Y.113, C:R.140, C:R.140 Water bridges: C:T.31, C:T.31 Salt bridges: C:K.112 AMP.24: 16 residues within 4Å: Chain D: V.17, M.18, 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 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:V.17, D:G.21, D:T.27, D:T.27, D:T.27, D:G.28, D:E.29, D:M.30, D:T.31, D:Y.113, D:R.140, D:R.140 Water bridges: D:T.31, 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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