SMTL ID : 5zwk.1

Crystal structure of Human liver fructose-1,6-bisphoaphatase complex with fructose-1,6-bisphophate and AMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

FBP.1: 19 residues within 4Å: Chain A: 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 Chain B: R.244 Ligands: MG.3, MG.4 22 PLIP interactions: 18 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:D.122, A:G.123, A:S.124, A:S.125, A:S.125, A:N.213, A:Y.245, A:Y.245, A:M.249, A:Y.265, A:K.275 Water bridges: A:S.125, A:Y.216, A:Y.245, A:G.247, A:Y.265, B:R.244, B:R.244, B:R.244 Salt bridges: A:K.275, A:K.275, B:R.244 FBP.5: 18 residues within 4Å: Chain A: R.244 Chain B: E.98, D.119, 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 Ligands: MG.7, MG.8 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.122, B:G.123, B:S.124, B:S.124, B:S.124, B:S.124, B:N.213, B:Y.216, B:M.249, B:Y.265, B:K.275 Water bridges: B:S.125, B:S.125 Salt bridges: B:K.275, B:K.275, A:R.244 FBP.9: 18 residues within 4Å: Chain C: E.98, D.119, 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.11, MG.12 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:D.122, C:D.122, C:G.123, C:S.124, C:N.213, C:Y.245, C:Y.245, C:M.249, C:Y.265, C:K.275 Water bridges: C:S.125 Salt bridges: C:K.275, D:R.244 FBP.13: 20 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, L.276, R.277, E.281 Ligands: MG.15, MG.16 21 PLIP interactions: 18 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:D.122, D:G.123, D:S.124, D:S.124, D:S.124, D:S.124, D:N.213, D:Y.245, D:M.249, D:K.275, D:E.281 Water bridges: D:S.125, D:S.125, D:S.125, D:K.275, C:R.244, C:R.244 Salt bridges: D:K.275, D:K.275, D:R.277, C:R.244

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 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 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:L.31, A:T.32, A:T.32, A:Y.114, A:Y.114 Water bridges: A:T.32, A:T.32 Salt bridges: A:K.113 AMP.6: 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 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:L.31, B:T.32, B:T.32, B:Y.114, B:Y.114 Water bridges: B:T.32, B:T.32 Salt bridges: B:K.113 AMP.10: 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 10 PLIP interactions: 10 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:Y.114 Water bridges: C:T.32 Salt bridges: C:K.113 AMP.14: 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 11 PLIP interactions: 11 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:T.32, D:Y.114, D:Y.114 Water bridges: D:T.32 Salt bridges: D:K.113

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.119, D.122, E.281 Ligands: FBP.1, MG.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.119, A:D.122, A:E.281 MG.4: 5 residues within 4Å: Chain A: D.119, L.121, D.122 Ligands: FBP.1, MG.3 4 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:D.119, A:L.121, FBP.1, H2O.3 MG.7: 6 residues within 4Å: Chain B: E.98, D.119, L.121, D.122 Ligands: FBP.5, MG.8 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.8: 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.11: 6 residues within 4Å: Chain C: E.98, D.119, L.121, D.122 Ligands: FBP.9, MG.12 3 PLIP interactions: 1 interactions with chain C, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: C:L.121, FBP.9, H2O.10 MG.12: 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.15: 5 residues within 4Å: Chain D: E.98, D.119, L.121 Ligands: FBP.13, MG.16 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:E.98, D:D.119, D:D.119, D:L.121, FBP.13 MG.16: 7 residues within 4Å: Chain D: E.98, D.119, D.122, R.277, E.281 Ligands: FBP.13, MG.15 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.119, D:D.122, D:E.281

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yunyuan, H. et al., Location of FBPase catalytic metal binding site: a combined experimental and theoretical study. To Be Published

Release Date

2019-05-15

Peptides

Fructose-1,6-bisphosphatase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Fructose-1,6-bisphosphatase 1

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