SMTL ID : 3uqe.1

Crystal structure of the Phosphofructokinase-2 mutant Y23D from Escherichia coli

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

ATP.1: 21 residues within 4Å: Chain A: K.185, N.187, S.224, L.225, G.226, P.227, G.229, P.243, S.248, A.254, G.255, M.258, V.280, G.283, S.284, T.287 Chain B: Q.228 Chain D: K.27 Ligands: MG.2, MG.3, POP.4 25 PLIP interactions: 19 interactions with chain A, 1 interactions with chain B, 5 interactions with chain D Hydrogen bonds: A:N.187, A:S.224, A:S.224, A:G.226, A:S.248, A:S.248, A:A.254, A:G.255, A:S.284 Water bridges: A:R.105, A:R.105, A:R.105, A:R.105, A:K.185, A:N.187, A:D.256, A:D.256, B:Q.228, D:K.27, D:K.27, D:K.27 Salt bridges: A:K.185, A:K.185, D:K.27, D:K.27 ATP.8: 21 residues within 4Å: Chain A: Q.228 Chain B: K.185, N.187, S.224, L.225, G.226, P.227, G.229, P.243, S.248, A.254, G.255, M.258, V.280, G.283, S.284, T.287 Chain C: K.27 Ligands: MG.5, POP.6, MG.7 25 PLIP interactions: 18 interactions with chain B, 2 interactions with chain A, 5 interactions with chain C Hydrogen bonds: B:N.187, B:S.224, B:S.224, B:G.226, B:S.248, B:A.254, B:G.255, B:S.284, B:T.287 Water bridges: B:R.105, B:R.105, B:N.187, B:G.253, B:G.253, B:G.253, B:D.256, A:Q.228, A:Q.228, C:K.27, C:K.27, C:K.27 Salt bridges: B:K.185, B:K.185, C:K.27, C:K.27 ATP.9: 21 residues within 4Å: Chain B: K.27 Chain C: K.185, N.187, S.224, L.225, G.226, P.227, G.229, P.243, S.248, A.254, G.255, M.258, V.280, G.283, S.284, T.287 Chain D: Q.228 Ligands: MG.10, MG.11, POP.12 26 PLIP interactions: 20 interactions with chain C, 5 interactions with chain B, 1 interactions with chain D Hydrogen bonds: C:N.187, C:S.224, C:S.224, C:G.226, C:S.248, C:S.248, C:A.254, C:G.255, C:S.284, C:T.287 Water bridges: C:R.105, C:R.105, C:R.105, C:R.105, C:K.185, C:N.187, C:D.256, C:D.256, B:K.27, B:K.27, B:K.27, D:Q.228 Salt bridges: C:K.185, C:K.185, B:K.27, B:K.27 ATP.16: 21 residues within 4Å: Chain A: K.27 Chain C: Q.228 Chain D: K.185, N.187, S.224, L.225, G.226, P.227, G.229, P.243, S.248, A.254, G.255, M.258, V.280, G.283, S.284, T.287 Ligands: MG.13, POP.14, MG.15 25 PLIP interactions: 18 interactions with chain D, 2 interactions with chain C, 5 interactions with chain A Hydrogen bonds: D:N.187, D:S.224, D:S.224, D:G.226, D:S.248, D:A.254, D:G.255, D:S.284 Water bridges: D:R.105, D:R.105, D:N.187, D:G.253, D:G.253, D:G.253, D:D.256, D:T.287, C:Q.228, C:Q.228, A:K.27, A:K.27, A:K.27 Salt bridges: D:K.185, D:K.185, A:K.27, A:K.27

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

MG.2: 2 residues within 4Å: Ligands: ATP.1, POP.4 No protein-ligand interaction detected (PLIP) MG.3: 4 residues within 4Å: Chain A: D.166, K.185, E.190 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain B: D.166 Ligands: ATP.8 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: N.187 Ligands: POP.6, ATP.8 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Ligands: ATP.9, POP.12 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain C: D.166, K.185, E.190 Ligands: ATP.9 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain D: D.166 Ligands: ATP.16 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain D: N.187 Ligands: POP.14, ATP.16 No protein-ligand interaction detected (PLIP)

4 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.4: 6 residues within 4Å: Chain A: N.187, K.189 Chain D: G.26, K.27 Ligands: ATP.1, MG.2 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:N.187, D:K.27 Water bridges: A:R.105, A:K.189, A:K.189, A:E.190, D:K.27 Salt bridges: A:K.189, A:K.189, D:K.27, D:K.27 POP.6: 5 residues within 4Å: Chain B: N.187 Chain C: G.26, K.27 Ligands: MG.7, ATP.8 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:N.187, C:K.27 Salt bridges: C:K.27, C:K.27 POP.12: 6 residues within 4Å: Chain B: G.26, K.27 Chain C: N.187, K.189 Ligands: ATP.9, MG.10 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:N.187, B:K.27 Water bridges: C:R.105, C:K.189, C:K.189, C:E.190, B:K.27 Salt bridges: C:K.189, C:K.189, B:K.27, B:K.27 POP.14: 5 residues within 4Å: Chain A: G.26, K.27 Chain D: N.187 Ligands: MG.15, ATP.16 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:N.187, A:K.27 Salt bridges: A:K.27, A:K.27

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pereira, H.M. et al., Structure of E. coli PFK2 mutant Y23D. To be Published

Release Date

2012-11-21

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