SMTL ID : 3umo.1 (1 other biounit)

Crystal structure of the Phosphofructokinase-2 from Escherichia coli in complex with Potassium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 2 residues within 4Å: Chain A: K.185 Ligands: ATP.3 No protein-ligand interaction detected (PLIP) MG.2: 3 residues within 4Å: Chain A: N.187 Ligands: ATP.3, ATP.7 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: N.187 Ligands: ATP.6, ATP.9 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Ligands: ATP.9 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain C: K.185 Ligands: ATP.13 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain C: N.187 Ligands: ATP.13, ATP.17 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain D: N.187 Ligands: ATP.16, ATP.19 No protein-ligand interaction detected (PLIP) MG.18: 1 residues within 4Å: Ligands: ATP.19 No protein-ligand interaction detected (PLIP)

8 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 20 residues within 4Å: Chain A: K.185, N.187, S.224, L.225, G.226, P.227, G.229, S.248, T.251, A.254, G.255, M.258, V.280, G.283, S.284, T.287 Chain B: K.27 Ligands: MG.1, MG.2, ATP.7 25 PLIP interactions: 18 interactions with chain A, 6 interactions with chain B, 1 interactions with chain D Hydrogen bonds: A:N.187, A:S.224, A:S.224, A:G.226, A:G.253, A:A.254, A:G.255 Water bridges: A:R.105, A:R.105, A:K.185, A:K.185, A:S.248, A:S.248, A:D.256, A:D.256, A:T.287, B:K.27, B:K.27, B:K.27, B:K.27, D:Q.228 Salt bridges: A:K.185, A:K.185, B:K.27, B:K.27 ATP.6: 8 residues within 4Å: Chain A: Y.23, G.26, K.27 Chain B: N.187, K.189 Chain C: E.102 Ligands: MG.5, ATP.9 16 PLIP interactions: 8 interactions with chain A, 2 interactions with chain C, 6 interactions with chain B Hydrogen bonds: A:K.27, C:E.102, B:N.187 Water bridges: A:K.27, A:K.27, A:K.27, C:S.100, B:R.105, B:K.189, B:K.189, B:E.190 Salt bridges: A:K.27, A:K.27, B:K.189 pi-Stacking: A:Y.23, A:Y.23 ATP.7: 8 residues within 4Å: Chain A: N.187, K.189 Chain B: Y.23, G.26, K.27 Chain D: E.102 Ligands: MG.2, ATP.3 16 PLIP interactions: 5 interactions with chain A, 9 interactions with chain B, 2 interactions with chain D Hydrogen bonds: A:N.187, B:K.27, D:E.102 Water bridges: A:K.189, A:E.190, A:E.190, B:Y.23, B:Y.23, B:K.27, B:K.27, D:S.100 Salt bridges: A:K.189, B:K.27, B:K.27 pi-Stacking: B:Y.23, B:Y.23 ATP.9: 21 residues within 4Å: Chain A: K.27 Chain B: K.185, N.187, S.224, L.225, G.226, P.227, G.229, S.248, T.251, G.253, A.254, G.255, M.258, V.280, G.283, S.284, T.287 Ligands: MG.5, ATP.6, MG.8 28 PLIP interactions: 22 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:N.187, B:S.224, B:S.224, B:L.225, B:G.226, B:S.248, B:G.253, B:A.254, B:G.255, B:S.284 Water bridges: B:R.105, B:R.105, B:K.185, B:K.185, B:S.248, B:S.248, B:D.256, B:D.256, B:D.256, B:T.287, A:K.27, A:K.27, A:K.27, A:K.27 Salt bridges: B:K.185, B:K.185, A:K.27, A:K.27 ATP.13: 20 residues within 4Å: Chain C: K.185, N.187, S.224, L.225, G.226, P.227, G.229, S.248, T.251, A.254, G.255, M.258, V.280, G.283, S.284, T.287 Chain D: K.27 Ligands: MG.11, MG.12, ATP.17 24 PLIP interactions: 17 interactions with chain C, 6 interactions with chain D, 1 interactions with chain B Hydrogen bonds: C:N.187, C:S.224, C:S.224, C:G.226, C:G.253, C:A.254, C:G.255 Water bridges: C:R.105, C:R.105, C:K.185, C:K.185, C:S.248, C:S.248, C:D.256, C:D.256, D:K.27, D:K.27, D:K.27, D:K.27, B:Q.228 Salt bridges: C:K.185, C:K.185, D:K.27, D:K.27 ATP.16: 8 residues within 4Å: Chain A: E.102 Chain C: Y.23, G.26, K.27 Chain D: N.187, K.189 Ligands: MG.15, ATP.19 17 PLIP interactions: 6 interactions with chain D, 10 interactions with chain C, 1 interactions with chain A Hydrogen bonds: D:N.187, C:K.27 Water bridges: D:R.105, D:K.189, D:K.189, D:E.190, C:Y.23, C:Y.23, C:K.27, C:K.27, C:K.27, A:S.100 Salt bridges: D:K.189, C:K.27, C:K.27 pi-Stacking: C:Y.23, C:Y.23 ATP.17: 8 residues within 4Å: Chain B: E.102 Chain C: N.187, K.189 Chain D: Y.23, G.26, K.27 Ligands: MG.12, ATP.13 17 PLIP interactions: 7 interactions with chain C, 9 interactions with chain D, 1 interactions with chain B Hydrogen bonds: C:N.187, D:K.27 Water bridges: C:K.189, C:E.190, C:E.190, C:E.190, C:E.190, D:Y.23, D:Y.23, D:K.27, D:K.27, B:S.100 Salt bridges: C:K.189, D:K.27, D:K.27 pi-Stacking: D:Y.23, D:Y.23 ATP.19: 21 residues within 4Å: Chain C: K.27 Chain D: K.185, N.187, S.224, L.225, G.226, P.227, G.229, S.248, T.251, G.253, A.254, G.255, M.258, V.280, G.283, S.284, T.287 Ligands: MG.15, ATP.16, MG.18 27 PLIP interactions: 21 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:N.187, D:S.224, D:S.224, D:L.225, D:G.226, D:S.248, D:G.253, D:A.254, D:G.255, D:S.284 Water bridges: D:R.105, D:R.105, D:K.185, D:K.185, D:S.248, D:S.248, D:D.256, D:D.256, D:D.256, C:K.27, C:K.27, C:K.27, C:K.27 Salt bridges: D:K.185, D:K.185, C:K.27, C:K.27

4 x K: POTASSIUM ION(Non-covalent)

K.4: 6 residues within 4Å: Chain A: S.250, V.252, A.286, N.289, G.291, R.293 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:V.252, A:A.286, A:N.289, A:G.291, A:R.293 K.10: 6 residues within 4Å: Chain B: S.250, V.252, A.286, N.289, G.291, R.293 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:A.286, B:N.289, B:G.291, B:R.293 K.14: 6 residues within 4Å: Chain C: S.250, V.252, A.286, N.289, G.291, R.293 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:V.252, C:A.286, C:N.289, C:G.291, C:R.293 K.20: 6 residues within 4Å: Chain D: S.250, V.252, A.286, N.289, G.291, R.293 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:A.286, D:N.289, D:G.291, D:R.293

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baez, M. et al., A Ribokinase Family Conserved Monovalent Cation Binding Site Enhances the MgATP-induced Inhibition in E. coli Phosphofructokinase-2. Biophys.J. (2013)

Release Date

2012-11-14

Peptides

6-phosphofructokinase isozyme 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

6-phosphofructokinase isozyme 2

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