SMTL ID : 7cvh.1

Human Fructose-1,6-bisphosphatase 1 in complex with geranylgeranyl diphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-tetramer

Ligands

4 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)

FBP.1: 20 residues within 4Å: Chain A: E.98, D.119, L.121, 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: MG.2, MG.3 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.122, A:D.122, A:G.123, A:S.124, A:S.124, A:N.213, A:Y.216, A:M.249, A:Y.265, A:K.275 Water bridges: A:S.125, B:R.244 Salt bridges: A:K.275, A:R.277, B:R.244 FBP.5: 20 residues within 4Å: Chain A: R.244 Chain B: E.98, D.119, L.121, D.122, G.123, S.124, S.125, N.213, Y.216, Y.245, G.247, S.248, M.249, Y.265, K.275, L.276, E.281 Ligands: MG.6, MG.7 19 PLIP interactions: 15 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.122, B:G.123, B:S.124, B:S.125, B:S.125, B:N.213, B:Y.245, B:Y.245, B:M.249, B:K.275 Water bridges: B:S.125, B:N.126, B:Y.216, B:Y.265, A:R.244, A:R.244, A:R.244 Salt bridges: B:K.275, A:R.244 FBP.9: 19 residues within 4Å: Chain C: E.98, D.119, L.121, D.122, G.123, S.124, N.213, Y.216, Y.245, G.247, S.248, M.249, Y.265, K.275, L.276, E.281 Chain D: R.244 Ligands: MG.10, MG.11 20 PLIP interactions: 17 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:D.122, C:G.123, C:S.124, C:S.124, C:S.124, C:N.213, C:Y.245, C:M.249, C:Y.265, C:K.275 Water bridges: C:S.124, C:S.125, C:S.125, C:S.125, C:Y.216, C:Y.265, D:R.244, D:R.244 Salt bridges: C:K.275, D:R.244 FBP.14: 18 residues within 4Å: Chain C: R.244 Chain D: E.98, D.119, L.121, D.122, G.123, S.124, N.213, Y.216, Y.245, G.247, S.248, M.249, Y.265, K.275, E.281 Ligands: MG.15, MG.16 19 PLIP interactions: 2 interactions with chain C, 17 interactions with chain D Water bridges: C:R.244, D:S.125, D:S.125, D:S.125, D:S.125, D:S.125 Salt bridges: C:R.244, D:K.275 Hydrogen bonds: D:L.121, D:D.122, D:D.122, D:G.123, D:S.124, D:N.213, D:Y.216, D:M.249, D:Y.265, D:Y.265, D:K.275

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.119, D.122, R.277, E.281 Ligands: FBP.1, MG.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.119, A:D.122, A:E.281, FBP.1 MG.3: 5 residues within 4Å: Chain A: E.98, D.119, L.121 Ligands: FBP.1, MG.2 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:E.98, A:D.119, A:L.121, FBP.1, H2O.7 MG.6: 6 residues within 4Å: Chain B: E.98, D.119, D.122, E.281 Ligands: FBP.5, MG.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.119, B:D.122, B:E.281, FBP.5 MG.7: 7 residues within 4Å: Chain B: E.98, D.119, L.121, D.122, S.124 Ligands: FBP.5, MG.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:E.98, B:D.119, B:D.119, B:L.121, FBP.5 MG.10: 6 residues within 4Å: Chain C: E.98, D.119, D.122, E.281 Ligands: FBP.9, MG.11 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:D.119, C:D.122, C:E.281, FBP.9 MG.11: 6 residues within 4Å: Chain C: E.98, D.119, L.121, D.122 Ligands: FBP.9, MG.10 5 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: C:E.98, C:D.119, C:L.121, FBP.9, H2O.22 MG.15: 5 residues within 4Å: Chain D: D.119, D.122, E.281 Ligands: FBP.14, MG.16 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:D.119, D:D.122, D:E.281, FBP.14 MG.16: 6 residues within 4Å: Chain D: E.98, D.119, L.121, D.122 Ligands: FBP.14, MG.15 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.98, D:D.119, D:L.121, H2O.32

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.4: 15 residues within 4Å: Chain A: V.18, E.21, G.22, A.25, G.27, T.28, G.29, E.30, L.31, T.32, K.113, Y.114, R.141, V.161, M.178 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:T.28, A:T.28, A:T.28, A:G.29, A:E.30, A:L.31, A:T.32, A:T.32, A:Y.114, A:Y.114 Water bridges: A:T.32, A:T.32, A:R.141, A:R.141 Salt bridges: A:K.113 AMP.8: 15 residues within 4Å: Chain B: V.18, E.21, G.22, A.25, G.27, T.28, G.29, E.30, L.31, T.32, K.113, Y.114, R.141, V.161, M.178 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:T.28, B:T.28, B:T.28, B:G.29, B:E.30, B:L.31, B:T.32, B:T.32, B:Y.114, B:Y.114, B:R.141 Water bridges: B:T.32, B:T.32, B:K.113, B:K.113 Salt bridges: B:K.113 AMP.12: 14 residues within 4Å: Chain C: V.18, E.21, G.22, A.25, G.27, T.28, G.29, E.30, L.31, T.32, K.113, Y.114, V.161, M.178 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:T.28, C:T.28, C:G.29, C:E.30, C:L.31, C:T.32, C:Y.114, C:R.141 Water bridges: C:T.32, C:T.32, C:R.141, C:R.141 Salt bridges: C:K.113 AMP.17: 15 residues within 4Å: Chain D: V.18, E.21, G.22, A.25, G.27, T.28, G.29, E.30, L.31, T.32, 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:L.31, D:T.32, D:Y.114, D:Y.114, D:R.141 Water bridges: D:T.32, D:T.32 Salt bridges: D:K.113

1 x GRG: GERANYLGERANYL DIPHOSPHATE(Non-covalent)

GRG.13: 14 residues within 4Å: Chain A: K.43, S.46, S.47, R.50, T.172, L.187, P.189 Chain B: R.50, P.189 Chain C: R.50, P.189, A.190 Chain D: R.50, P.189 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:R.50, A:L.187, A:P.189, B:R.50, B:R.50, B:P.189

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Y. et al., The structural basis for GGPP activation on the enzymatic activities FBP1. To Be Published

Release Date

2021-09-08

Peptides

Fructose-1,6-bisphosphatase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

D
D

Fructose-1,6-bisphosphatase 1

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