SMTL ID : 2f3d.1

Mechanism of displacement of a catalytically essential loop from the active site of fructose-1,6-bisphosphatase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 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.122, G.123, S.124, 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 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.123, A:S.124, A:N.213, A:Y.245, A:M.249, A:K.275 Water bridges: A:D.69, A:S.125, A:S.125, A:S.125, A:S.125, A:S.125, A:Y.216, A:K.275, A:K.275, B:R.244, B:R.244 Salt bridges: A:K.275, B:R.244 F6P.7: 16 residues within 4Å: Chain A: R.244 Chain B: D.122, G.123, S.124, N.213, Y.216, Y.245, G.247, S.248, M.249, Y.265, K.275, L.276, R.277, E.281 Ligands: PO4.8 19 PLIP interactions: 16 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.123, B:S.124, B:N.213, B:Y.245, B:M.249, B:K.275 Water bridges: B:D.69, B:S.125, B:S.125, B:S.125, B:S.125, B:S.125, B:Y.216, B:K.275, B:K.275, A:R.244, A:R.244 Salt bridges: B:K.275, A:R.244 F6P.13: 16 residues within 4Å: Chain C: D.122, G.123, S.124, 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: PO4.14 23 PLIP interactions: 20 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:D.122, C:G.123, C:S.124, C:N.213, C:Y.216, C:Y.245, C:Y.245, C:M.249, C:Y.265, C:K.275 Water bridges: C:D.69, C:S.125, C:S.125, C:S.125, C:S.125, C:S.125, C:Y.216, C:K.275, C:K.275, D:R.244, D:R.244 Salt bridges: C:K.275, D:R.244 F6P.19: 16 residues within 4Å: Chain C: R.244 Chain D: D.122, G.123, S.124, N.213, Y.216, Y.245, G.247, S.248, M.249, Y.265, K.275, L.276, R.277, E.281 Ligands: PO4.20 22 PLIP interactions: 19 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:G.123, D:S.124, D:N.213, D:Y.216, D:Y.245, D:Y.245, D:M.249, D:Y.265, D:K.275 Water bridges: D:D.69, D:S.125, D:S.125, D:S.125, D:S.125, D:S.125, D:Y.216, D:K.275, D:K.275, C:R.244, C:R.244 Salt bridges: D:K.275, C:R.244

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

PO4.2: 13 residues within 4Å: Chain A: D.69, E.98, D.119, L.121, D.122, G.123, S.124, R.277, E.281 Ligands: F6P.1, ZN.3, ZN.4, ZN.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.121, A:G.123, A:S.124 Water bridges: A:D.69, A:S.124 Salt bridges: A:R.277 PO4.8: 13 residues within 4Å: Chain B: D.69, E.98, D.119, L.121, D.122, G.123, S.124, R.277, E.281 Ligands: F6P.7, ZN.9, ZN.10, ZN.11 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.121, B:G.123, B:S.124 Water bridges: B:D.69, B:S.124 Salt bridges: B:R.277 PO4.14: 13 residues within 4Å: Chain C: D.69, E.98, D.119, L.121, D.122, G.123, S.124, R.277, E.281 Ligands: F6P.13, ZN.15, ZN.16, ZN.17 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:L.121, C:D.122, C:G.123, C:S.124, C:E.281 Water bridges: C:D.69, C:D.69, C:E.99, C:S.124 Salt bridges: C:R.277 PO4.20: 13 residues within 4Å: Chain D: D.69, E.98, D.119, L.121, D.122, G.123, S.124, R.277, E.281 Ligands: F6P.19, ZN.21, ZN.22, ZN.23 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:L.121, D:G.123, D:S.124 Water bridges: D:E.99, D:S.124 Salt bridges: D:R.277

12 x ZN: ZINC ION(Non-covalent)

ZN.3: 7 residues within 4Å: Chain A: E.98, E.99, D.119, L.121 Ligands: PO4.2, ZN.4, ZN.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.98, A:D.119, A:L.121, H2O.1 ZN.4: 6 residues within 4Å: Chain A: D.119, D.122, R.277, E.281 Ligands: PO4.2, ZN.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.119, A:D.122, A:E.281 ZN.5: 6 residues within 4Å: Chain A: N.65, D.69, E.98, R.277 Ligands: PO4.2, ZN.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.69, A:E.98, H2O.5 ZN.9: 7 residues within 4Å: Chain B: E.98, E.99, D.119, L.121 Ligands: PO4.8, ZN.10, ZN.11 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.98, B:D.119, B:L.121, H2O.8 ZN.10: 6 residues within 4Å: Chain B: D.119, D.122, R.277, E.281 Ligands: PO4.8, ZN.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.119, B:D.122, B:E.281 ZN.11: 6 residues within 4Å: Chain B: N.65, D.69, E.98, R.277 Ligands: PO4.8, ZN.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.69, B:E.98, H2O.12 ZN.15: 7 residues within 4Å: Chain C: E.98, E.99, D.119, L.121 Ligands: PO4.14, ZN.16, ZN.17 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.98, C:D.119, C:L.121, H2O.15 ZN.16: 6 residues within 4Å: Chain C: D.119, D.122, R.277, E.281 Ligands: PO4.14, ZN.15 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.119, C:D.122, C:E.281 ZN.17: 6 residues within 4Å: Chain C: N.65, D.69, E.98, R.277 Ligands: PO4.14, ZN.15 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.69, C:E.98, H2O.19 ZN.21: 7 residues within 4Å: Chain D: E.98, E.99, D.119, L.121 Ligands: PO4.20, ZN.22, ZN.23 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.98, D:D.119, D:L.121, H2O.22 ZN.22: 6 residues within 4Å: Chain D: D.119, D.122, R.277, E.281 Ligands: PO4.20, ZN.21 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.119, D:D.122, D:E.281 ZN.23: 6 residues within 4Å: Chain D: N.65, D.69, E.98, R.277 Ligands: PO4.20, ZN.21 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.69, D:E.98, H2O.26

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.6: 14 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, 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:M.31, A:T.32, A:T.32, A:T.32, A:Y.114, A:Y.114, A:R.141 Salt bridges: A:K.113 AMP.12: 14 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, K.113, Y.114, R.141, M.178 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:T.28, B:T.28, B:T.28, B:G.29, B:E.30, B:M.31, B:T.32, B:T.32, B:T.32, B:Y.114, B:Y.114, B:R.141 Salt bridges: B:K.113 AMP.18: 14 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, M.178 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:T.28, C:T.28, C:T.28, C:G.29, C:E.30, C:M.31, C:T.32, C:T.32, C:Y.114, C:Y.114, C:R.141 Salt bridges: C:K.113 AMP.24: 14 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, K.113, Y.114, R.141, M.178 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:T.28, 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 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

2006-04-25

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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