SMTL ID : 3cqd.1

Structure of the tetrameric inhibited form of phosphofructokinase-2 from Escherichia coli

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain B: N.187 Ligands: ATP.5, ATP.7 No protein-ligand interaction detected (PLIP) MG.2: 4 residues within 4Å: Chain A: D.166, K.185 Chain B: K.27 Ligands: ATP.4 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain A: N.187 Ligands: ATP.4, ATP.8 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain A: K.27 Chain B: K.185 Ligands: ATP.7 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain D: N.187 Ligands: ATP.13, ATP.15 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain C: D.166, K.185 Chain D: K.27 Ligands: ATP.12 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain C: N.187 Ligands: ATP.12, ATP.16 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain C: K.27 Chain D: K.185 Ligands: ATP.15 No protein-ligand interaction detected (PLIP)

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

ATP.4: 22 residues within 4Å: Chain A: K.185, N.187, S.224, L.225, G.226, P.227, G.229, P.243, S.248, T.251, G.253, A.254, G.255, M.258, V.280, G.283, S.284, T.287 Chain B: K.27 Ligands: MG.2, MG.3, ATP.8 30 PLIP interactions: 24 interactions with chain A, 5 interactions with chain B, 1 interactions with chain D Hydrogen bonds: A:N.187, A:S.224, A:S.224, A:L.225, A:G.226, A:S.248, A:S.248, A:G.253, A:A.254, A:G.255, A:S.284, A:T.287 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:T.251, A:D.256, 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.5: 11 residues within 4Å: Chain A: Y.23, P.24, G.26, K.27 Chain B: N.187, K.189, G.226, P.227, T.251 Ligands: MG.1, ATP.7 15 PLIP interactions: 8 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:N.187, A:G.26, A:K.27 Water bridges: B:R.105, B:R.105, B:E.190, B:E.190, B:E.190, B:T.251, A:P.24, A:K.27, A:K.27 Salt bridges: B:K.189, A:K.27, A:K.27 ATP.7: 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.1, ATP.5, MG.6 29 PLIP interactions: 23 interactions with chain B, 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: B:N.187, B:S.224, B:S.224, B:L.225, B:G.226, B:S.248, B:S.248, B:G.253, B:G.255, B:S.284 Water bridges: B:R.105, 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:D.256, B:D.256, A:K.27, A:K.27, C:Q.228, C:Q.228 Salt bridges: B:K.185, B:K.185, A:K.27, A:K.27 ATP.8: 11 residues within 4Å: Chain A: N.187, K.189, G.226, P.227, T.251 Chain B: Y.23, P.24, G.26, K.27 Ligands: MG.3, ATP.4 14 PLIP interactions: 6 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:K.27, A:N.187 Water bridges: B:P.24, B:K.27, B:K.27, A:R.105, A:R.105, A:K.189, A:K.189, A:E.190, A:T.251 Salt bridges: B:K.27, B:K.27, A:K.189 ATP.12: 22 residues within 4Å: Chain C: K.185, N.187, S.224, L.225, G.226, P.227, G.229, P.243, S.248, T.251, G.253, A.254, G.255, M.258, V.280, G.283, S.284, T.287 Chain D: K.27 Ligands: MG.10, MG.11, ATP.16 29 PLIP interactions: 23 interactions with chain C, 1 interactions with chain B, 5 interactions with chain D Hydrogen bonds: C:N.187, C:S.224, C:S.224, C:L.225, C:G.226, C:S.248, C:S.248, C:G.253, C:A.254, C:G.255, C:S.284 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:T.251, C:D.256, B:Q.228, D:K.27, D:K.27, D:K.27 Salt bridges: C:K.185, C:K.185, D:K.27, D:K.27 ATP.13: 11 residues within 4Å: Chain C: Y.23, P.24, G.26, K.27 Chain D: N.187, K.189, G.226, P.227, T.251 Ligands: MG.9, ATP.15 14 PLIP interactions: 6 interactions with chain D, 8 interactions with chain C Hydrogen bonds: D:N.187, C:Y.23, C:G.26, C:K.27 Water bridges: D:R.105, D:R.105, D:R.105, D:E.190, C:P.24, C:K.27, C:K.27 Salt bridges: D:K.189, C:K.27, C:K.27 ATP.15: 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.9, ATP.13, MG.14 29 PLIP interactions: 23 interactions with chain D, 4 interactions with chain C, 2 interactions with chain A Hydrogen bonds: D:N.187, D:S.224, D:S.224, D:L.225, D:G.226, D:S.248, D:S.248, D:G.253, D:G.255, D:S.284 Water bridges: D:R.105, 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:D.256, D:D.256, C:K.27, C:K.27, A:Q.228, A:Q.228 Salt bridges: D:K.185, D:K.185, C:K.27, C:K.27 ATP.16: 11 residues within 4Å: Chain C: N.187, K.189, G.226, P.227, T.251 Chain D: Y.23, P.24, G.26, K.27 Ligands: MG.11, ATP.12 17 PLIP interactions: 8 interactions with chain D, 9 interactions with chain C Hydrogen bonds: D:K.27, C:N.187 Water bridges: D:Y.23, D:Y.23, D:P.24, D:K.27, D:K.27, C:R.105, C:R.105, C:R.105, C:K.189, C:K.189, C:E.190, C:E.190 Salt bridges: D:K.27, D:K.27, C:K.189

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cabrera, R. et al., Crystallographic structure of phosphofructokinase-2 from Escherichia coli in complex with two ATP molecules. Implications for substrate inhibition. J.Mol.Biol. (2008)

Release Date

2008-09-16

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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