SMTL ID : 1yxi.1

R-State AMP Complex Reveals Initial Steps of the Quaternary Transition of Fructose-1,6-bisphosphatase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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: PO4.3, MG.5 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.121, A:G.122, A:N.212, A:Y.215, A:Y.244, A:Y.244, A:M.248, A:Y.264, A:K.274 Water bridges: A:D.68, A:S.124, A:S.124, A:Y.215, A:Y.264, B:R.243, B:R.243 Salt bridges: A:K.274, B:R.243 F6P.7: 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: PO4.9, MG.11 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.121, B:G.122, B:N.212, B:Y.215, B:Y.244, B:Y.244, B:M.248, B:Y.264, B:K.274 Water bridges: B:D.68, B:S.124, B:S.124, B:Y.215, B:Y.264, A:R.243, A:R.243 Salt bridges: B:K.274, A:R.243 F6P.13: 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: PO4.15, MG.17 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:D.121, C:G.122, C:N.212, C:Y.244, C:M.248, C:K.274 Water bridges: C:D.68, C:E.97, C:S.124, C:S.124, C:Y.215, C:Y.264, D:R.243, D:R.243 Salt bridges: C:K.274, D:R.243 F6P.19: 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: PO4.21, MG.23 15 PLIP interactions: 12 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:D.121, D:G.122, D:N.212, D:Y.244, D:M.248, D:K.274 Water bridges: D:D.68, D:S.124, D:S.124, D:Y.215, D:Y.264, C:R.243, C:R.243 Salt bridges: D:K.274, C:R.243

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

PO4.2: 7 residues within 4Å: Chain A: G.26, T.27, G.28, E.29, M.30, K.112, Y.113 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.27, A:T.27, A:G.28, A:E.29, A:M.30, A:Y.113 Salt bridges: A:K.112 PO4.3: 13 residues within 4Å: Chain A: D.68, D.74, E.97, D.118, L.120, D.121, G.122, S.123, E.280 Ligands: F6P.1, MG.4, MG.5, MG.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.120, A:D.121, A:D.121, A:G.122, A:S.123 PO4.8: 7 residues within 4Å: Chain B: G.26, T.27, G.28, E.29, M.30, K.112, Y.113 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.27, B:T.27, B:G.28, B:E.29, B:M.30, B:Y.113 Salt bridges: B:K.112 PO4.9: 13 residues within 4Å: Chain B: D.68, D.74, E.97, D.118, L.120, D.121, G.122, S.123, E.280 Ligands: F6P.7, MG.10, MG.11, MG.12 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.120, B:D.121, B:D.121, B:G.122, B:S.123 PO4.14: 7 residues within 4Å: Chain C: G.26, T.27, G.28, E.29, M.30, K.112, Y.113 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:T.27, C:T.27, C:G.28, C:E.29, C:M.30 Water bridges: C:Y.113 Salt bridges: C:K.112 PO4.15: 13 residues within 4Å: Chain C: D.68, D.74, E.97, D.118, L.120, D.121, G.122, S.123, E.280 Ligands: F6P.13, MG.16, MG.17, MG.18 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.68, C:L.120, C:G.122, C:S.123, C:E.280, C:E.280 Water bridges: C:D.68, C:E.97 PO4.20: 7 residues within 4Å: Chain D: G.26, T.27, G.28, E.29, M.30, K.112, Y.113 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.27, D:T.27, D:G.28, D:E.29, D:M.30 Water bridges: D:Y.113 Salt bridges: D:K.112 PO4.21: 13 residues within 4Å: Chain D: D.68, D.74, E.97, D.118, L.120, D.121, G.122, S.123, E.280 Ligands: F6P.19, MG.22, MG.23, MG.24 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.68, D:L.120, D:D.121, D:G.122, D:S.123

12 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 7 residues within 4Å: Chain A: E.97, D.118, L.120, D.121 Ligands: PO4.3, MG.5, MG.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.97, A:D.118, A:L.120 MG.5: 6 residues within 4Å: Chain A: D.118, D.121, E.280 Ligands: F6P.1, PO4.3, MG.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.118, A:D.121, A:E.280 MG.6: 5 residues within 4Å: Chain A: N.64, D.68, E.97 Ligands: PO4.3, MG.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.68, A:E.97 MG.10: 7 residues within 4Å: Chain B: E.97, D.118, L.120, D.121 Ligands: PO4.9, MG.11, MG.12 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.97, B:D.118, B:L.120 MG.11: 6 residues within 4Å: Chain B: D.118, D.121, E.280 Ligands: F6P.7, PO4.9, MG.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.118, B:D.121, B:E.280 MG.12: 5 residues within 4Å: Chain B: N.64, D.68, E.97 Ligands: PO4.9, MG.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.68, B:E.97 MG.16: 7 residues within 4Å: Chain C: E.97, D.118, L.120, D.121 Ligands: PO4.15, MG.17, MG.18 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.97, C:D.118, C:L.120 MG.17: 6 residues within 4Å: Chain C: D.118, D.121, E.280 Ligands: F6P.13, PO4.15, MG.16 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.118, C:D.121, C:E.280 MG.18: 5 residues within 4Å: Chain C: N.64, D.68, E.97 Ligands: PO4.15, MG.16 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.68, C:E.97 MG.22: 7 residues within 4Å: Chain D: E.97, D.118, L.120, D.121 Ligands: PO4.21, MG.23, MG.24 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.97, D:D.118, D:L.120 MG.23: 6 residues within 4Å: Chain D: D.118, D.121, E.280 Ligands: F6P.19, PO4.21, MG.22 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.118, D:D.121, D:E.280 MG.24: 5 residues within 4Å: Chain D: N.64, D.68, E.97 Ligands: PO4.21, MG.22 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.68, D:E.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Iancu, C.V. et al., R-state AMP complex reveals initial steps of the quaternary transition of fructose-1,6-bisphosphatase. J.Biol.Chem. (2005)

Release Date

2005-03-15

Peptides

Fructose-1,6-bisphosphatase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Fructose-1,6-bisphosphatase

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