SMTL ID : 4he1.1

Crystal structure of human muscle fructose-1,6-bisphosphatase Q32R mutant complex with fructose-6-phosphate and phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.23 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.121, G.122, N.212, Y.215, Y.244, G.246, S.247, M.248, Y.264, K.274, L.275, E.280 Chain B: R.243 Ligands: PO4.2, MG.3 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.121, A:G.122, A:N.212, A:Y.215, A:Y.244, A:M.248, A:Y.264, A:Y.264, A:K.274, A:E.280 Water bridges: A:S.124, A:Y.244, A:G.246, A:V.249, B:R.243 Salt bridges: A:K.274, B:R.243 F6P.6: 15 residues within 4Å: Chain A: R.243 Chain B: D.121, G.122, N.212, Y.215, Y.244, G.246, S.247, M.248, Y.264, K.274, L.275, E.280 Ligands: PO4.7, MG.8 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.121, B:G.122, B:N.212, B:Y.215, B:Y.244, B:M.248, B:Y.264, B:Y.264, B:K.274, B:E.280 Water bridges: B:S.124, B:Y.244, B:G.246, B:V.249, A:R.243 Salt bridges: B:K.274, A:R.243 F6P.11: 15 residues within 4Å: Chain C: D.121, G.122, N.212, Y.215, Y.244, G.246, S.247, M.248, Y.264, K.274, L.275, E.280 Chain D: R.243 Ligands: PO4.12, MG.13 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:D.121, C:G.122, C:N.212, C:Y.244, C:M.248, C:Y.264, C:K.274, C:E.280 Water bridges: C:S.124, C:Y.244, C:G.246, C:V.249, D:R.243 Salt bridges: C:K.274, D:R.243 F6P.16: 15 residues within 4Å: Chain C: R.243 Chain D: D.121, G.122, N.212, Y.215, Y.244, G.246, S.247, M.248, Y.264, K.274, L.275, E.280 Ligands: PO4.17, MG.18 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:D.121, D:G.122, D:N.212, D:Y.244, D:M.248, D:Y.264, D:K.274, D:E.280 Water bridges: D:S.124, D:Y.244, D:G.246, D:V.249, C:R.243 Salt bridges: D:K.274, C:R.243

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

PO4.2: 10 residues within 4Å: Chain A: E.97, D.118, L.120, D.121, G.122, S.123, E.280 Ligands: F6P.1, MG.3, MG.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.97, A:G.122, A:S.123, A:S.123 Water bridges: A:L.120 PO4.7: 10 residues within 4Å: Chain B: E.97, D.118, L.120, D.121, G.122, S.123, E.280 Ligands: F6P.6, MG.8, MG.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.97, B:G.122, B:S.123, B:S.123 Water bridges: B:L.120 PO4.12: 10 residues within 4Å: Chain C: E.97, D.118, L.120, D.121, G.122, S.123, E.280 Ligands: F6P.11, MG.13, MG.14 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.97, C:G.122, C:S.123, C:S.123 Water bridges: C:L.120 PO4.17: 10 residues within 4Å: Chain D: E.97, D.118, L.120, D.121, G.122, S.123, E.280 Ligands: F6P.16, MG.18, MG.19 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.97, D:G.122, D:S.123, D:S.123 Water bridges: D:L.120

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 7 residues within 4Å: Chain A: E.97, D.118, D.121, E.280 Ligands: F6P.1, PO4.2, MG.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.97, A:D.118, A:D.121, A:E.280 MG.4: 7 residues within 4Å: Chain A: E.97, E.98, D.118, L.120, D.121 Ligands: PO4.2, MG.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.97, A:D.118, A:L.120, H2O.3, H2O.3 MG.8: 7 residues within 4Å: Chain B: E.97, D.118, D.121, E.280 Ligands: F6P.6, PO4.7, MG.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.97, B:D.118, B:D.121, B:E.280 MG.9: 7 residues within 4Å: Chain B: E.97, E.98, D.118, L.120, D.121 Ligands: PO4.7, MG.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.97, B:D.118, B:L.120, H2O.8, H2O.8 MG.13: 7 residues within 4Å: Chain C: E.97, D.118, D.121, E.280 Ligands: F6P.11, PO4.12, MG.14 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.97, C:D.118, C:D.121, C:E.280 MG.14: 7 residues within 4Å: Chain C: E.97, E.98, D.118, L.120, D.121 Ligands: PO4.12, MG.13 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.97, C:D.118, C:L.120, H2O.13, H2O.13 MG.18: 7 residues within 4Å: Chain D: E.97, D.118, D.121, E.280 Ligands: F6P.16, PO4.17, MG.19 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.97, D:D.118, D:D.121, D:E.280 MG.19: 7 residues within 4Å: Chain D: E.97, E.98, D.118, L.120, D.121 Ligands: PO4.17, MG.18 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.97, D:D.118, D:L.120, H2O.18, H2O.18

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 7 residues within 4Å: Chain A: A.130, S.131, V.245 Chain B: A.130, S.131, V.245 Ligands: CL.10 Ligand excluded by PLIP CL.10: 7 residues within 4Å: Chain A: A.130, S.131, V.245 Chain B: A.130, S.131, V.245 Ligands: CL.5 Ligand excluded by PLIP CL.15: 7 residues within 4Å: Chain C: A.130, S.131, V.245 Chain D: A.130, S.131, V.245 Ligands: CL.20 Ligand excluded by PLIP CL.20: 7 residues within 4Å: Chain C: A.130, S.131, V.245 Chain D: A.130, S.131, V.245 Ligands: CL.15 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, R. et al., Crystal Structures of Human Muscle Fructose-1,6-Bisphosphatase: Novel Quaternary States, Enhanced AMP Affinity, and Allosteric Signal Transmission Pathway. Plos One (2013)

Release Date

2013-10-09

Peptides

Fructose-1,6-bisphosphatase isozyme 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Fructose-1,6-bisphosphatase isozyme 2

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