SMTL ID : 3uqd.1

Crystal structure of the Phosphofructokinase-2 from Escherichia coli in complex with substrates and products

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-tetramer

Ligands

4 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, G.253, A.254, G.255, M.258, V.280, G.283, S.284, T.287 Ligands: MG.3, MG.4, ATP.9 21 PLIP interactions: 21 interactions with chain A 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 Water bridges: A:R.105, A:R.105, A:R.105, A:K.185, A:S.248, A:S.248, A:D.256, A:D.256, A:D.256 Salt bridges: A:K.185, A:K.185 ATP.8: 11 residues within 4Å: Chain B: Q.21, Y.23, P.24, G.26, K.27 Chain C: A.99, S.100, E.102 Chain D: N.187 Ligands: ATP.13, MG.16 14 PLIP interactions: 8 interactions with chain D, 5 interactions with chain B, 1 interactions with chain C Hydrogen bonds: D:R.105, D:N.187, B:Q.21, B:K.27, C:A.99 Water bridges: D:K.189, D:E.190, D:E.190, D:E.190, D:E.190, D:T.251, B:Y.23 pi-Stacking: B:Y.23, B:Y.23 ATP.9: 10 residues within 4Å: Chain A: N.187 Chain B: A.99, S.100, E.102 Chain C: Q.21, Y.23, G.26, K.27 Ligands: ATP.1, MG.4 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:N.187, C:Q.21, C:K.27 Water bridges: A:R.105, A:R.105, A:R.105, A:E.190, A:E.190 pi-Stacking: C:Y.23, C:Y.23 ATP.13: 20 residues within 4Å: 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: ATP.8, MG.15, MG.16 19 PLIP interactions: 16 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:N.187, D:S.224, D:S.224, D:S.224, D:L.225, D:G.226, D:S.248, D:G.255 Water bridges: D:R.105, D:R.105, D:N.187, D:S.248, D:D.256, D:D.256, B:K.27, B:K.27 Salt bridges: D:K.185, D:K.185, B:K.27

2 x F6P: 6-O-phosphono-beta-D-fructofuranose(Non-covalent)

F6P.2: 13 residues within 4Å: Chain A: D.14, G.38, G.39, N.43, R.90, N.92, R.105, V.107, G.138, S.139, D.256 Chain C: K.27, R.29 22 PLIP interactions: 16 interactions with chain A, 6 interactions with chain C Hydrogen bonds: A:D.14, A:G.39, A:N.43, A:N.43, A:N.92, A:R.105, A:S.139, A:S.139, A:D.256 Water bridges: A:D.14, A:D.14, A:R.90, A:G.253, A:G.253, A:D.256, C:K.27, C:K.27, C:K.27, C:K.27 Salt bridges: A:R.90, C:K.27, C:R.29 F6P.14: 15 residues within 4Å: Chain B: K.27, R.29 Chain D: S.12, D.14, G.38, G.39, G.40, N.43, R.90, N.92, R.105, V.107, G.138, S.139, D.256 16 PLIP interactions: 12 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:S.12, D:D.14, D:G.39, D:G.39, D:N.43, D:N.92, D:R.105, D:S.139, D:S.139, B:K.27 Water bridges: D:G.253, D:D.256, B:K.27 Salt bridges: D:R.90, B:K.27, B:R.29

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

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

2 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)

FBP.5: 19 residues within 4Å: Chain B: S.12, D.14, G.38, G.39, G.40, N.43, R.90, N.92, R.105, G.138, S.139, T.251, V.252, G.253, A.254, D.256 Chain D: K.27, R.29 Ligands: MG.7 21 PLIP interactions: 16 interactions with chain B, 5 interactions with chain D Hydrogen bonds: B:S.12, B:D.14, B:G.39, B:G.39, B:N.43, B:N.92, B:R.105, B:S.139, B:S.139, B:T.251, B:G.253, B:A.254, D:K.27 Water bridges: B:R.90, B:R.105, D:K.27 Salt bridges: B:R.90, B:R.105, D:K.27, D:K.27, D:R.29 FBP.10: 18 residues within 4Å: Chain A: K.27, R.29 Chain C: S.12, D.14, G.38, G.39, G.40, N.43, R.90, N.92, R.105, V.107, G.138, S.139, V.252, G.253, A.254, D.256 24 PLIP interactions: 19 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:S.12, C:D.14, C:G.39, C:G.39, C:N.43, C:N.92, C:S.139, C:S.139, C:G.253, C:A.254, C:G.255 Water bridges: C:A.10, C:G.40, C:G.40, C:R.105, C:R.105, C:T.251, A:K.27, A:R.29 Salt bridges: C:R.90, C:R.105, A:K.27, A:K.27, A:R.29

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.6: 17 residues within 4Å: Chain B: 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 Ligands: MG.7 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.187, B:S.224, B:L.225, B:G.226, B:S.248 Water bridges: B:R.105, B:D.166, B:K.185, B:E.190, B:T.251, B:T.251, B:G.255, A:Q.228, A:Q.228 Salt bridges: B:K.185, B:K.185 ADP.11: 18 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, A.254, G.255, M.258, V.280, G.283, S.284, T.287 Ligands: MG.12 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:N.187, C:S.224, C:S.224, C:G.226, C:S.248, C:S.248 Water bridges: C:E.190, C:G.255 Salt bridges: C:K.185, C:K.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murillo-Lopez, J. et al., Studying the phosphoryl transfer mechanism of theE. coliphosphofructokinase-2: from X-ray structure to quantum mechanics/molecular mechanics simulations. Chem Sci (2019)

Release Date

2012-11-28

Peptides

6-phosphofructokinase isozyme 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

6-phosphofructokinase isozyme 2

Related Entries With Identical Sequence