SMTL ID : 5xz7.1

Crystal Structure of Phosphofructokinase from Staphylococcus aureus in complex with adenylylimidodiphosphate, the ATP analogue

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: S.9, Y.41, R.72, C.73, G.104, S.105, G.108 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.73, A:G.108 Water bridges: A:S.9, A:A.71 GOL.2: 4 residues within 4Å: Chain A: Y.38, H.39, D.48, H.50 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.39 GOL.3: 6 residues within 4Å: Chain A: A.261 Chain B: F.137, D.142, W.181 Ligands: PEG.8, GOL.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.142 GOL.4: 5 residues within 4Å: Chain A: R.268, I.293 Chain B: D.310, S.312, L.313 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.310, A:R.268 Water bridges: B:S.312, B:L.316, A:R.268 GOL.5: 8 residues within 4Å: Chain A: T.190, I.191, E.202, I.203, K.206, Y.314, N.318, E.324 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:I.191, A:I.191, A:E.202, A:K.206, A:Y.314, A:N.318 Water bridges: A:K.206 GOL.6: 5 residues within 4Å: Chain A: R.173, D.174, E.224, G.225 Ligands: F6P.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.174 Water bridges: A:R.173, A:E.224 GOL.9: 7 residues within 4Å: Chain B: S.9, Y.41, R.72, C.73, G.104, S.105, G.108 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:C.73, B:G.108 Water bridges: B:S.9, B:A.71 GOL.10: 4 residues within 4Å: Chain B: Y.38, H.39, D.48, H.50 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.39 GOL.11: 6 residues within 4Å: Chain A: F.137, D.142, W.181 Chain B: A.261 Ligands: GOL.3, PEG.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.142 GOL.12: 5 residues within 4Å: Chain A: D.310, S.312, L.313 Chain B: R.268, I.293 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.310, B:R.268 Water bridges: A:S.312, A:L.316, B:R.268 GOL.13: 8 residues within 4Å: Chain B: T.190, I.191, E.202, I.203, K.206, Y.314, N.318, E.324 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:I.191, B:I.191, B:E.202, B:K.206, B:Y.314, B:N.318 Water bridges: B:K.206 GOL.14: 5 residues within 4Å: Chain B: R.173, D.174, E.224, G.225 Ligands: F6P.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.174 Water bridges: B:R.173, B:E.224

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

F6P.7: 9 residues within 4Å: Chain A: R.72, D.129, M.171, G.172, R.173, E.224, H.251, R.254 Ligands: GOL.6 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: 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:R.72, A:T.127, A:D.129, A:R.173, A:R.173 Salt bridges: A:R.72, A:H.251, A:R.254 F6P.15: 9 residues within 4Å: Chain B: R.72, D.129, M.171, G.172, R.173, E.224, H.251, R.254 Ligands: GOL.14 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: 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:R.72, B:T.127, B:D.129, B:R.173, B:R.173 Salt bridges: B:R.72, B:H.251, B:R.254

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 7 residues within 4Å: Chain A: R.268, I.288, N.291 Chain B: F.137, W.181, D.310 Ligands: GOL.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.268, A:N.291 Water bridges: A:R.268, A:R.268 PEG.16: 7 residues within 4Å: Chain A: F.137, W.181, D.310 Chain B: R.268, I.288, N.291 Ligands: GOL.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.268, B:N.291 Water bridges: B:R.268, B:R.268

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

2019-03-13

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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