SMTL ID : 4kxp.1

Crystal Structure of AMP complexes of Porcine Liver Fructose-1,6-bisphosphatase Mutant I10D in T-state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 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.122, G.123, N.213, Y.216, Y.245, G.247, S.248, M.249, Y.265, K.275, L.276, R.277, E.281 Chain B: R.244 Ligands: PO4.2 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.213, A:Y.216, A:Y.245, A:M.249, A:Y.265, A:K.275, A:R.277 Water bridges: A:S.125, B:R.244 Salt bridges: A:K.275, B:R.244 F6P.6: 15 residues within 4Å: Chain A: R.244 Chain B: D.122, G.123, N.213, Y.216, Y.245, G.247, S.248, M.249, Y.265, K.275, L.276, R.277, E.281 Ligands: PO4.7 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.122, B:G.123, B:N.213, B:Y.216, B:Y.245, B:M.249, B:K.275, B:R.277 Water bridges: B:S.125, B:S.125 Salt bridges: B:K.275, A:R.244 F6P.11: 15 residues within 4Å: Chain C: D.122, G.123, N.213, Y.216, Y.245, G.247, S.248, M.249, Y.265, K.275, L.276, R.277, E.281 Chain D: R.244 Ligands: PO4.12 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:N.213, C:Y.216, C:Y.245, C:M.249, C:Y.265, C:K.275, C:R.277 Water bridges: C:S.125, D:R.244 Salt bridges: C:K.275, D:R.244 F6P.16: 15 residues within 4Å: Chain C: R.244 Chain D: D.122, G.123, N.213, Y.216, Y.245, G.247, S.248, M.249, Y.265, K.275, L.276, R.277, E.281 Ligands: PO4.17 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.122, D:G.123, D:N.213, D:Y.216, D:Y.245, D:M.249, D:K.275, D:R.277 Water bridges: D:S.125, D:S.125 Salt bridges: D:K.275, C:R.244

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

PO4.2: 11 residues within 4Å: Chain A: E.98, D.119, L.121, D.122, G.123, S.124, R.277, E.281 Ligands: F6P.1, MG.3, MG.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.98, A:D.119, A:G.123, A:S.124, A:S.124 Water bridges: A:R.277 Salt bridges: A:R.277 PO4.7: 11 residues within 4Å: Chain B: E.98, D.119, L.121, D.122, G.123, S.124, R.277, E.281 Ligands: F6P.6, MG.8, MG.9 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.123, B:S.124, B:S.124 Water bridges: B:D.75, B:E.98 Salt bridges: B:R.277 PO4.12: 11 residues within 4Å: Chain C: E.98, D.119, L.121, D.122, G.123, S.124, R.277, E.281 Ligands: F6P.11, MG.13, MG.14 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:E.98, C:D.119, C:G.123, C:S.124, C:S.124 Water bridges: C:R.277 Salt bridges: C:R.277 PO4.17: 11 residues within 4Å: Chain D: E.98, D.119, L.121, D.122, G.123, S.124, R.277, E.281 Ligands: F6P.16, MG.18, MG.19 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.123, D:S.124, D:S.124 Water bridges: D:D.75, D:E.98 Salt bridges: D:R.277

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.119, D.122, R.277, E.281 Ligands: PO4.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.119, A:D.122, A:E.281 MG.4: 6 residues within 4Å: Chain A: E.98, D.119, P.120, L.121, D.122 Ligands: PO4.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.98, A:D.119, A:L.121 MG.8: 4 residues within 4Å: Chain B: D.119, D.122, E.281 Ligands: PO4.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.119, B:D.122, B:E.281 MG.9: 7 residues within 4Å: Chain B: D.75, E.98, E.99, D.119, P.120, L.121 Ligands: PO4.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.75, B:L.121 MG.13: 5 residues within 4Å: Chain C: D.119, D.122, R.277, E.281 Ligands: PO4.12 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.119, C:D.122, C:E.281 MG.14: 6 residues within 4Å: Chain C: E.98, D.119, P.120, L.121, D.122 Ligands: PO4.12 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.98, C:D.119, C:L.121 MG.18: 4 residues within 4Å: Chain D: D.119, D.122, E.281 Ligands: PO4.17 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.119, D:D.122, D:E.281 MG.19: 7 residues within 4Å: Chain D: D.75, E.98, E.99, D.119, P.120, L.121 Ligands: PO4.17 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.75, D:L.121

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.5: 15 residues within 4Å: Chain A: V.18, E.21, G.22, A.25, G.27, T.28, G.29, E.30, M.31, T.32, K.113, Y.114, R.141, V.161, M.178 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:T.28, A:T.28, A:T.28, A:G.29, A:E.30, A:E.30, A:M.31, A:T.32, A:Y.114, A:Y.114 Water bridges: A:T.32, A:R.141 Salt bridges: A:K.113 AMP.10: 16 residues within 4Å: Chain B: V.18, E.21, G.22, A.25, G.27, T.28, G.29, E.30, M.31, T.32, L.35, K.113, Y.114, R.141, V.161, M.178 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:T.28, B:T.28, B:G.29, B:E.30, B:M.31, B:T.32, B:T.32, B:Y.114, B:Y.114, B:R.141 Water bridges: B:T.32 Salt bridges: B:K.113 AMP.15: 15 residues within 4Å: Chain C: V.18, E.21, G.22, A.25, G.27, T.28, G.29, E.30, M.31, T.32, K.113, Y.114, R.141, V.161, M.178 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:T.28, C:T.28, C:T.28, C:G.29, C:E.30, C:E.30, C:M.31, C:T.32, C:Y.114, C:Y.114 Water bridges: C:T.32, C:R.141 Salt bridges: C:K.113 AMP.20: 16 residues within 4Å: Chain D: V.18, E.21, G.22, A.25, G.27, T.28, G.29, E.30, M.31, T.32, L.35, K.113, Y.114, R.141, V.161, M.178 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:T.28, D:T.28, D:G.29, D:E.30, D:M.31, D:T.32, D:T.32, D:Y.114, D:Y.114, D:R.141 Water bridges: D:T.32 Salt bridges: D:K.113

Links

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Citation

Gao, Y. et al., Mechanism of Displacement of a Catalytically Essential Loop from the Active Site of Mammalian Fructose-1,6-bisphosphatase. Biochemistry (2013)

Release Date

2013-07-24

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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