SMTL ID : 4h46.1

Crystal Structure of AMP complexes of NEM modified Porcine Liver Fructose-1,6-bisphosphatase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 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: MG.2, PO4.3 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.121, A:D.121, A:G.122, A:N.212, A:Y.244, A:M.248, A:K.274 Water bridges: A:Y.215, A:Y.215, A:Y.215, A:V.249, A:Y.264, A:K.274, 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: MG.7, PO4.8 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.121, B:D.121, B:G.122, B:N.212, B:Y.244, B:M.248, B:K.274 Water bridges: B:Y.215, B:Y.215, B:Y.215, B:V.249, B:Y.264, B:K.274, 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: MG.12, PO4.13 18 PLIP interactions: 16 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:D.121, C:D.121, C:G.122, C:N.212, C:Y.215, C:Y.244, C:Y.244, C:M.248, C:Y.264, C:K.274 Water bridges: C:Y.215, C:Y.215, C:V.249, C:Y.264, C:K.274, 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: MG.17, PO4.18 18 PLIP interactions: 16 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:D.121, D:D.121, D:G.122, D:N.212, D:Y.215, D:Y.244, D:Y.244, D:M.248, D:Y.264, D:K.274 Water bridges: D:Y.215, D:Y.215, D:V.249, D:Y.264, D:K.274, C:R.243 Salt bridges: D:K.274, C:R.243

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: E.97, D.118, D.121, E.280 Ligands: F6P.1, PO4.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.97, A:D.118, A:D.121, A:E.280 MG.7: 6 residues within 4Å: Chain B: E.97, D.118, D.121, E.280 Ligands: F6P.6, PO4.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.97, B:D.118, B:D.121, B:E.280 MG.12: 6 residues within 4Å: Chain C: E.97, D.118, D.121, E.280 Ligands: F6P.11, PO4.13 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.97, C:D.118, C:D.121, C:E.280 MG.17: 6 residues within 4Å: Chain D: E.97, D.118, D.121, E.280 Ligands: F6P.16, PO4.18 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.97, D:D.118, D:D.121, D:E.280

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

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

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.4: 16 residues within 4Å: Chain A: V.17, E.20, G.21, A.24, G.26, T.27, G.28, E.29, M.30, T.31, L.34, K.112, Y.113, R.140, V.160, M.177 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:T.27, A:T.27, A:T.27, A:G.28, A:E.29, A:M.30, A:T.31, A:T.31, A:Y.113, A:Y.113, A:R.140 Water bridges: A:T.31, A:K.112, A:K.112 Salt bridges: A:K.112 AMP.9: 16 residues within 4Å: Chain B: V.17, E.20, G.21, A.24, G.26, T.27, G.28, E.29, M.30, T.31, L.34, K.112, Y.113, R.140, V.160, M.177 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:T.27, B:T.27, B:T.27, B:G.28, B:E.29, B:M.30, B:T.31, B:T.31, B:Y.113, B:Y.113, B:R.140 Water bridges: B:T.31, B:K.112, B:K.112 Salt bridges: B:K.112 AMP.14: 16 residues within 4Å: Chain C: V.17, E.20, G.21, A.24, G.26, T.27, G.28, E.29, M.30, T.31, L.34, K.112, Y.113, R.140, V.160, M.177 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:T.27, C:T.27, C:T.27, C:T.27, C:G.28, C:E.29, C:E.29, C:M.30, C:T.31, C:Y.113, C:Y.113, C:R.140 Water bridges: C:T.31, C:K.112, C:K.112 Salt bridges: C:K.112 AMP.19: 16 residues within 4Å: Chain D: V.17, E.20, G.21, A.24, G.26, T.27, G.28, E.29, M.30, T.31, L.34, K.112, Y.113, R.140, V.160, M.177 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:T.27, D:T.27, D:T.27, D:T.27, D:G.28, D:E.29, D:E.29, D:M.30, D:T.31, D:Y.113, D:Y.113, D:R.140 Water bridges: D:T.31, D:K.112, D:K.112 Salt bridges: D:K.112

4 x NEN: 1-ETHYL-PYRROLIDINE-2,5-DIONE(Non-covalent)

NEN.5: 9 residues within 4Å: Chain A: S.124, N.125, D.127, C.128, V.130 Chain B: I.208, R.243, R.254, Y.258 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.208 NEN.10: 9 residues within 4Å: Chain A: I.208, R.243, R.254, Y.258 Chain B: S.124, N.125, D.127, C.128, V.130 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.208 NEN.15: 9 residues within 4Å: Chain C: S.124, N.125, D.127, C.128, V.130 Chain D: I.208, R.243, R.254, Y.258 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.208 NEN.20: 9 residues within 4Å: Chain C: I.208, R.243, R.254, Y.258 Chain D: S.124, N.125, D.127, C.128, V.130 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, Y. et al., Fluorescent 2',3'-O-(2,4,6-trinitrophenyl) (TNP)-AMP Is an Active Site Inhibitor for Porcine Liver Fructose-1,6-bisphosphatase Rather Than Allosteric Inhibitor. To be Published

Release Date

2013-09-18

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

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