SMTL ID : 5xz8.1

Crystal Structure of Phosphofructokinase from Staphylococcus aureus in complex with adenylylimidodiphosphate (the ATP analog) and fructose-6-phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

F6P.1: 9 residues within 4Å: Chain A: R.72, D.129, M.171, G.172, R.173, E.224, H.251, R.254 Ligands: ANP.6 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:T.127, A:T.127, A:D.129, A:G.172, A:R.173, A:R.173, A:E.224, A:R.254 Water bridges: A:G.11, A:G.11, A:R.72, A:R.72, A:R.72, A:R.72, A:D.129 Salt bridges: A:R.72, A:H.251, A:R.254 F6P.7: 9 residues within 4Å: Chain B: R.72, D.129, M.171, G.172, R.173, E.224, H.251, R.254 Ligands: ANP.12 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:T.127, B:T.127, B:D.129, B:G.172, B:R.173, B:R.173, B:E.224, B:R.254 Water bridges: B:G.11, B:G.11, B:R.72, B:R.72, B:R.72, B:R.72, B:D.129 Salt bridges: B:R.72, B:H.251, B:R.254

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: D.153 Chain B: Q.62, S.257, R.263 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.257, B:R.263 Water bridges: B:Q.62 GOL.3: 5 residues within 4Å: Chain A: Y.38, H.39, D.48, H.50, Y.69 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.39, A:H.50 GOL.4: 5 residues within 4Å: Chain A: F.137, D.142, W.181 Chain B: A.261 Ligands: GOL.10 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.142 Water bridges: B:A.261, B:N.291 GOL.8: 4 residues within 4Å: Chain A: Q.62, S.257, R.263 Chain B: D.153 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.257, A:R.263 Water bridges: A:Q.62 GOL.9: 5 residues within 4Å: Chain B: Y.38, H.39, D.48, H.50, Y.69 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.39, B:H.50 GOL.10: 5 residues within 4Å: Chain A: A.261 Chain B: F.137, D.142, W.181 Ligands: GOL.4 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:A.261, A:N.291 Hydrogen bonds: B:D.142

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.5: 1 residues within 4Å: Ligands: ANP.6 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Ligands: ANP.12 No protein-ligand interaction detected (PLIP)

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.6: 19 residues within 4Å: Chain A: S.9, G.10, G.11, Y.41, R.72, C.73, P.74, F.76, K.77, G.102, D.103, G.104, S.105, R.107, G.108, T.127, R.173 Ligands: F6P.1, MG.5 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.9, A:G.11, A:C.73, A:C.73, A:G.102, A:G.102, A:G.104, A:S.105, A:R.173, A:R.173 Water bridges: A:S.9, A:G.10, A:Y.41, A:K.77, A:D.103, A:T.127, A:T.127 ANP.12: 19 residues within 4Å: Chain B: S.9, G.10, G.11, Y.41, R.72, C.73, P.74, F.76, K.77, G.102, D.103, G.104, S.105, R.107, G.108, T.127, R.173 Ligands: F6P.7, MG.11 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:S.9, B:G.11, B:C.73, B:C.73, B:G.102, B:G.102, B:G.104, B:S.105, B:R.173, B:R.173 Water bridges: B:S.9, B:G.10, B:Y.41, B:K.77, B:D.103, B:T.127, B:T.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tian, T. et al., Structural Insights into the Regulation of Staphylococcus aureus Phosphofructokinase by Tetramer-Dimer Conversion. Biochemistry (2018)

Release Date

2019-02-27

Peptides

ATP-dependent 6-phosphofructokinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ATP-dependent 6-phosphofructokinase

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