SMTL ID : 4he2.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 14 residues within 4Å: Chain A: V.17, K.20, G.21, A.24, G.26, T.27, G.28, E.29, L.30, T.31, K.112, Y.113, V.160, T.177 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:T.27, A:T.27, A:G.28, A:E.29, A:L.30, A:T.31, A:T.31, A:Y.113, A:Y.113 Water bridges: A:T.31, A:T.31, A:K.112, A:T.177 Salt bridges: A:K.112 AMP.8: 14 residues within 4Å: Chain B: V.17, K.20, G.21, A.24, G.26, T.27, G.28, E.29, L.30, T.31, K.112, Y.113, V.160, T.177 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:T.27, B:T.27, B:G.28, B:E.29, B:L.30, B:T.31, B:T.31, B:Y.113, B:Y.113 Water bridges: B:T.31, B:T.31, B:K.112, B:T.177 Salt bridges: B:K.112 AMP.15: 14 residues within 4Å: Chain C: V.17, K.20, G.21, A.24, G.26, T.27, G.28, E.29, L.30, T.31, K.112, Y.113, V.160, T.177 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:T.27, C:T.27, C:G.28, C:E.29, C:L.30, C:T.31, C:Y.113, C:Y.113 Water bridges: C:T.31, C:T.31, C:K.112 Salt bridges: C:K.112 AMP.22: 14 residues within 4Å: Chain D: V.17, K.20, G.21, A.24, G.26, T.27, G.28, E.29, L.30, T.31, K.112, Y.113, V.160, T.177 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:T.27, D:T.27, D:G.28, D:E.29, D:L.30, D:T.31, D:Y.113, D:Y.113 Water bridges: D:T.31, D:T.31, D:K.112 Salt bridges: D:K.112

4 x PO3: PHOSPHITE ION(Non-covalent)

PO3.2: 11 residues within 4Å: Chain A: E.97, D.118, L.120, D.121, G.122, S.123, E.280 Ligands: MG.3, ZN.4, MG.5, MG.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.122, A:S.123 Water bridges: A:L.120, A:S.123, A:S.123, A:S.123, A:S.124 PO3.9: 11 residues within 4Å: Chain B: E.97, D.118, L.120, D.121, G.122, S.123, E.280 Ligands: MG.10, ZN.11, MG.12, MG.13 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.122, B:S.123 Water bridges: B:L.120, B:S.123, B:S.123, B:S.123, B:S.124 PO3.16: 11 residues within 4Å: Chain C: E.97, D.118, L.120, D.121, G.122, S.123, E.280 Ligands: MG.17, ZN.18, MG.19, MG.20 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.122, C:S.123 Water bridges: C:L.120, C:S.123, C:S.123, C:S.123, C:S.124 PO3.23: 11 residues within 4Å: Chain D: E.97, D.118, L.120, D.121, G.122, S.123, E.280 Ligands: MG.24, ZN.25, MG.26, MG.27 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.122, D:S.123 Water bridges: D:L.120, D:S.123, D:S.123, D:S.123, D:S.124

12 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: D.118, D.121, E.280 Ligands: PO3.2, ZN.4, MG.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.118, A:D.121, A:E.280, H2O.10 MG.5: 10 residues within 4Å: Chain A: D.74, E.97, E.98, D.118, L.120, D.121 Ligands: PO3.2, MG.3, ZN.4, MG.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.97, A:D.118, A:L.120, H2O.1, H2O.3 MG.6: 3 residues within 4Å: Chain A: E.97 Ligands: PO3.2, MG.5 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.97, H2O.3, H2O.4, H2O.5, H2O.10 MG.10: 6 residues within 4Å: Chain B: D.118, D.121, E.280 Ligands: PO3.9, ZN.11, MG.12 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.118, B:D.121, B:E.280, H2O.20 MG.12: 10 residues within 4Å: Chain B: D.74, E.97, E.98, D.118, L.120, D.121 Ligands: PO3.9, MG.10, ZN.11, MG.13 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.97, B:D.118, B:L.120, H2O.11, H2O.13 MG.13: 3 residues within 4Å: Chain B: E.97 Ligands: PO3.9, MG.12 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.97, H2O.13, H2O.14, H2O.15, H2O.20 MG.17: 6 residues within 4Å: Chain C: D.118, D.121, E.280 Ligands: PO3.16, ZN.18, MG.19 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.118, C:D.121, C:E.280, H2O.29 MG.19: 10 residues within 4Å: Chain C: D.74, E.97, E.98, D.118, L.120, D.121 Ligands: PO3.16, MG.17, ZN.18, MG.20 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.97, C:D.118, C:L.120, H2O.21, H2O.23 MG.20: 3 residues within 4Å: Chain C: E.97 Ligands: PO3.16, MG.19 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.97, H2O.23, H2O.24, H2O.25, H2O.30 MG.24: 6 residues within 4Å: Chain D: D.118, D.121, E.280 Ligands: PO3.23, ZN.25, MG.26 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.118, D:D.121, D:E.280, H2O.39 MG.26: 10 residues within 4Å: Chain D: D.74, E.97, E.98, D.118, L.120, D.121 Ligands: PO3.23, MG.24, ZN.25, MG.27 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.97, D:D.118, D:L.120, H2O.31, H2O.32 MG.27: 3 residues within 4Å: Chain D: E.97 Ligands: PO3.23, MG.26 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:E.97, H2O.32, H2O.34, H2O.35, H2O.40

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 7 residues within 4Å: Chain A: E.97, D.118, D.121, E.280 Ligands: PO3.2, MG.3, MG.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.97, A:D.118, A:E.280 ZN.11: 7 residues within 4Å: Chain B: E.97, D.118, D.121, E.280 Ligands: PO3.9, MG.10, MG.12 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.97, B:D.118, B:E.280 ZN.18: 7 residues within 4Å: Chain C: E.97, D.118, D.121, E.280 Ligands: PO3.16, MG.17, MG.19 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.97, C:D.118, C:E.280 ZN.25: 7 residues within 4Å: Chain D: E.97, D.118, D.121, E.280 Ligands: PO3.23, MG.24, MG.26 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.97, D:D.118, D:E.280

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

CL.7: 7 residues within 4Å: Chain A: A.130, S.131, V.245 Chain B: A.130, S.131, V.245 Ligands: CL.14 Ligand excluded by PLIP CL.14: 7 residues within 4Å: Chain A: A.130, S.131, V.245 Chain B: A.130, S.131, V.245 Ligands: CL.7 Ligand excluded by PLIP CL.21: 7 residues within 4Å: Chain C: A.130, S.131, V.245 Chain D: A.130, S.131, V.245 Ligands: CL.28 Ligand excluded by PLIP CL.28: 7 residues within 4Å: Chain C: A.130, S.131, V.245 Chain D: A.130, S.131, V.245 Ligands: CL.21 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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