SMTL ID : 2f3b.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 1.80 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, S.124, N.213, Y.216, Y.245, G.247, S.248, M.249, Y.265, K.275, R.277, E.281 Chain B: R.244 Ligands: PO4.3 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.123, A:S.124, A:N.213, A:Y.216, A:Y.245, A:Y.245, A:M.249, A:Y.265, A:K.275 Water bridges: A:S.125, A:S.125, A:S.125, A:S.125, A:S.125, A:Y.216, A:Y.265, A:R.277, B:R.244 Salt bridges: A:K.275, B:R.244 F6P.7: 15 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, R.277, E.281 Ligands: PO4.9 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.123, B:S.124, B:N.213, B:Y.216, B:Y.245, B:Y.245, B:M.249, B:Y.265, B:K.275 Water bridges: B:S.125, B:S.125, B:S.125, B:S.125, B:S.125, B:Y.216, B:Y.265, B:R.277, A:R.244 Salt bridges: B:K.275, A:R.244 F6P.13: 15 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, R.277, E.281 Chain D: R.244 Ligands: PO4.15 19 PLIP interactions: 17 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:D.122, C:G.123, C:S.124, C:N.213, C:Y.245, C:M.249, 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:Y.265, C:R.277, D:R.244 Salt bridges: C:K.275, D:R.244 F6P.19: 15 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, R.277, E.281 Ligands: PO4.21 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.123, D:S.124, D:N.213, D:Y.245, D:M.249, D:K.275 Water bridges: D:S.125, D:S.125, D:S.125, D:S.125, D:S.125, D:Y.216, D:Y.265, D:R.277, C:R.244 Salt bridges: D:K.275, C:R.244

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

PO4.2: 7 residues within 4Å: Chain A: G.27, T.28, G.29, E.30, M.31, K.113, Y.114 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.28, A:G.29, A:E.30, A:M.31, A:Y.114 Salt bridges: A:K.113 PO4.3: 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.4, ZN.5, ZN.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.123, A:S.124 Water bridges: A:E.99, A:S.124, A:S.124, A:K.275 Salt bridges: A:R.277 PO4.8: 7 residues within 4Å: Chain B: G.27, T.28, G.29, E.30, M.31, K.113, Y.114 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.28, B:G.29, B:E.30, B:M.31, B:Y.114 Salt bridges: B:K.113 PO4.9: 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.10, ZN.11, ZN.12 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.123, B:S.124 Water bridges: B:E.99, B:S.124, B:S.124, B:K.275 Salt bridges: B:R.277 PO4.14: 7 residues within 4Å: Chain C: G.27, T.28, G.29, E.30, M.31, K.113, Y.114 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.28, C:G.29, C:E.30, C:M.31 Water bridges: C:Y.114 Salt bridges: C:K.113 PO4.15: 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.16, ZN.17, ZN.18 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:L.121, C:G.123, C:S.124, C:E.281, C:E.281 Water bridges: C:D.69, C:D.69, C:D.119, C:S.124, C:S.124, C:K.275, C:R.277 Salt bridges: C:R.277 PO4.20: 7 residues within 4Å: Chain D: G.27, T.28, G.29, E.30, M.31, K.113, Y.114 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.28, D:G.29, D:E.30, D:M.31 Water bridges: D:Y.114 Salt bridges: D:K.113 PO4.21: 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.22, ZN.23, ZN.24 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.123, D:S.124 Water bridges: D:S.124, D:S.124, D:K.275 Salt bridges: D:R.277

12 x ZN: ZINC ION(Non-covalent)

ZN.4: 8 residues within 4Å: Chain A: E.98, E.99, D.119, L.121, D.122 Ligands: PO4.3, ZN.5, ZN.6 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.5: 6 residues within 4Å: Chain A: D.119, D.122, R.277, E.281 Ligands: PO4.3, ZN.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.119, A:D.122, A:E.281 ZN.6: 6 residues within 4Å: Chain A: N.65, D.69, E.98, R.277 Ligands: PO4.3, ZN.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.69, A:E.98, H2O.4, H2O.5 ZN.10: 8 residues within 4Å: Chain B: E.98, E.99, D.119, L.121, D.122 Ligands: PO4.9, ZN.11, ZN.12 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.11: 6 residues within 4Å: Chain B: D.119, D.122, R.277, E.281 Ligands: PO4.9, ZN.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.119, B:D.122, B:E.281 ZN.12: 6 residues within 4Å: Chain B: N.65, D.69, E.98, R.277 Ligands: PO4.9, ZN.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.69, B:E.98, H2O.11, H2O.11 ZN.16: 8 residues within 4Å: Chain C: E.98, E.99, D.119, L.121, D.122 Ligands: PO4.15, ZN.17, ZN.18 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.98, C:D.119, C:L.121, H2O.14 ZN.17: 6 residues within 4Å: Chain C: D.119, D.122, R.277, E.281 Ligands: PO4.15, ZN.16 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.119, C:D.122, C:E.281 ZN.18: 6 residues within 4Å: Chain C: N.65, D.69, E.98, R.277 Ligands: PO4.15, ZN.16 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.69, C:E.98, H2O.18, H2O.18 ZN.22: 8 residues within 4Å: Chain D: E.98, E.99, D.119, L.121, D.122 Ligands: PO4.21, ZN.23, ZN.24 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.98, D:D.119, D:L.121, H2O.21 ZN.23: 6 residues within 4Å: Chain D: D.119, D.122, R.277, E.281 Ligands: PO4.21, ZN.22 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.119, D:D.122, D:E.281 ZN.24: 6 residues within 4Å: Chain D: N.65, D.69, E.98, R.277 Ligands: PO4.21, ZN.22 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.69, D:E.98, H2O.24, H2O.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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

Related Entries With Identical Sequence