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

Crystal structure of the Phosphofructokinase-2 from Escherichia coli in complex with Cesium and ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

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

ATP.1: 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.2, MG.3, ATP.7 27 PLIP interactions: 22 interactions with chain A, 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: A:N.187, A:S.224, A:S.224, A:G.226, A:S.248, A:A.254, A:G.255 Water bridges: A:R.105, A:R.105, A:R.105, A:K.185, A:K.185, A:K.185, A:S.248, A:S.248, A:G.253, A:G.253, A:G.253, A:D.256, A:T.287, 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 15 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A, 3 interactions with chain C Hydrogen bonds: B:N.187, A:K.27, C:E.102 Water bridges: B:R.105, B:K.189, B:K.189, B:E.190, A:K.27, C:S.100, C:E.102 Salt bridges: B:K.189, A:K.27, A:K.27 pi-Stacking: A:Y.23, A:Y.23 ATP.7: 7 residues within 4Å: Chain A: N.187 Chain B: Y.23, G.26, K.27 Chain D: E.102 Ligands: ATP.1, MG.3 12 PLIP interactions: 1 interactions with chain D, 6 interactions with chain A, 5 interactions with chain B Hydrogen bonds: D:E.102, A:N.187, B:K.27 Water bridges: A:R.105, A:E.190, A:E.190, A:E.190, A:T.251 Salt bridges: 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, P.243, S.248, T.251, A.254, G.255, M.258, V.280, G.283, S.284, T.287 Ligands: MG.5, ATP.6, MG.8 23 PLIP interactions: 21 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.187, B:S.224, B:S.224, B:G.226, B:S.248, B:A.254, B:G.255 Water bridges: B:R.105, B:R.105, B:R.105, B:K.185, B:K.185, B:K.185, B:S.248, B:S.248, B:G.253, B:G.253, B:G.253, B:T.287 Salt bridges: B:K.185, B:K.185, A:K.27, A:K.27 ATP.11: 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.12, MG.13, ATP.17 26 PLIP interactions: 21 interactions with chain C, 1 interactions with chain B, 4 interactions with chain D Hydrogen bonds: C:N.187, C:S.224, C:S.224, C:G.226, C:S.248, C:A.254, C:G.255 Water bridges: C:R.105, C:R.105, C:R.105, C:K.185, C:K.185, C:K.185, C:S.248, C:S.248, C:G.253, C:G.253, C:G.253, C:D.256, B:Q.228, D:K.27, D:K.27 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 15 PLIP interactions: 2 interactions with chain A, 6 interactions with chain D, 7 interactions with chain C Water bridges: A:S.100, A:E.102, D:R.105, D:K.189, D:K.189, D:E.190, C:Y.23, C:K.27 Hydrogen bonds: D:N.187, C:K.27 Salt bridges: D:K.189, C:K.27, C:K.27 pi-Stacking: C:Y.23, C:Y.23 ATP.17: 7 residues within 4Å: Chain B: E.102 Chain C: N.187 Chain D: Y.23, G.26, K.27 Ligands: ATP.11, MG.13 14 PLIP interactions: 6 interactions with chain D, 8 interactions with chain C Hydrogen bonds: D:K.27, C:N.187 Water bridges: D:Y.23, C:R.105, C:E.190, C:E.190, C:E.190, C:E.190, C:T.251, C:T.251 Salt bridges: 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, P.243, S.248, T.251, A.254, G.255, M.258, V.280, G.283, S.284, T.287 Ligands: MG.15, ATP.16, MG.18 22 PLIP interactions: 20 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:N.187, D:S.224, D:S.224, D:G.226, D:S.248, D:A.254, D:G.255 Water bridges: D:R.105, D:R.105, D:R.105, D:K.185, D:K.185, D:K.185, D:S.248, D:S.248, D:G.253, D:G.253, D:G.253 Salt bridges: D:K.185, D:K.185, C:K.27, C:K.27

8 x MG: MAGNESIUM ION(Non-covalent)

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

4 x CS: CESIUM ION(Non-covalent)

CS.4: 6 residues within 4Å: Chain A: S.250, V.252, A.286, N.289, G.291, R.293 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:V.252, A:A.286 CS.10: 6 residues within 4Å: Chain B: S.250, V.252, A.286, N.289, G.291, R.293 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:V.252, B:N.289, B:G.291 CS.14: 6 residues within 4Å: Chain C: S.250, V.252, A.286, N.289, G.291, R.293 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:V.252, C:A.286 CS.20: 6 residues within 4Å: Chain D: S.250, V.252, A.286, N.289, G.291, R.293 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:V.252, D:N.289, D:G.291

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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