SMTL ID : 7lw1.1

Human phosphofructokinase-1 liver type bound to activator NA-11

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x YG1: N-{(11S)-2-[2-(5-hydroxypent-1-yn-1-yl)phenyl]-4H,10H-pyrazolo[5,1-c][1,4]benzoxazepin-7-yl}acetamide(Non-covalent)

YG1.1: 27 residues within 4Å: Chain A: M.174, D.179, L.182, Y.214, V.218, A.307, F.308, I.311, K.315, L.338, G.340, N.341, Q.342, S.343, F.537, S.541, D.542, V.545, N.546, Y.578, V.582, P.669, F.670, N.673, L.712, W.740, L.744 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.182, A:F.308, A:I.311, A:I.311, A:K.315, A:F.537, A:F.670, A:W.740, A:L.744, A:L.744 Hydrogen bonds: A:D.179, A:D.542, A:Y.578 pi-Stacking: A:F.308, A:F.308, A:F.670, A:W.740 YG1.5: 27 residues within 4Å: Chain B: M.174, D.179, L.182, Y.214, V.218, A.307, F.308, I.311, K.315, L.338, G.340, N.341, Q.342, S.343, F.537, S.541, D.542, V.545, N.546, Y.578, V.582, P.669, F.670, N.673, L.712, W.740, L.744 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.182, B:F.308, B:I.311, B:I.311, B:K.315, B:F.537, B:F.670, B:W.740, B:L.744, B:L.744 Hydrogen bonds: B:D.179, B:D.179, B:Y.578 pi-Stacking: B:F.308, B:F.308, B:F.670, B:W.740 YG1.9: 27 residues within 4Å: Chain C: M.174, D.179, L.182, Y.214, V.218, A.307, F.308, I.311, K.315, L.338, G.340, N.341, Q.342, S.343, F.537, S.541, D.542, V.545, N.546, Y.578, V.582, P.669, F.670, N.673, L.712, W.740, L.744 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:L.182, C:F.308, C:I.311, C:I.311, C:K.315, C:F.537, C:F.670, C:W.740, C:L.744, C:L.744 Hydrogen bonds: C:D.179, C:D.542, C:Y.578 pi-Stacking: C:F.308, C:F.308, C:F.670, C:W.740 YG1.13: 27 residues within 4Å: Chain D: M.174, D.179, L.182, Y.214, V.218, A.307, F.308, I.311, K.315, L.338, G.340, N.341, Q.342, S.343, F.537, S.541, D.542, V.545, N.546, Y.578, V.582, P.669, F.670, N.673, L.712, W.740, L.744 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:L.182, D:F.308, D:I.311, D:I.311, D:K.315, D:F.537, D:F.670, D:W.740, D:L.744, D:L.744 Hydrogen bonds: D:D.179, D:D.179, D:Y.578 pi-Stacking: D:F.308, D:F.308, D:F.670, D:W.740

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

FBP.2: 17 residues within 4Å: Chain A: A.409, R.470, G.497, F.498, T.527, I.528, S.529, N.531, M.572, G.574, E.628, H.660, Q.663, R.734 Chain B: T.562, R.565, R.654 15 PLIP interactions: 2 interactions with chain B, 13 interactions with chain A Salt bridges: B:R.565, B:R.654, A:R.470, A:R.470, A:H.660, A:R.734 Hydrogen bonds: A:R.470, A:R.470, A:T.527, A:S.529, A:N.531, A:G.574, A:E.628, A:E.628, A:Q.663 FBP.6: 17 residues within 4Å: Chain A: T.562, R.565, R.654 Chain B: A.409, R.470, G.497, F.498, T.527, I.528, S.529, N.531, M.572, G.574, E.628, H.660, Q.663, R.734 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.470, B:R.470, B:T.527, B:T.527, B:S.529, B:N.531, B:G.574, B:E.628, B:E.628, B:Q.663 Salt bridges: B:R.470, B:R.470, B:H.660, B:R.734, A:R.565, A:R.654 FBP.10: 17 residues within 4Å: Chain C: A.409, R.470, G.497, F.498, T.527, I.528, S.529, N.531, M.572, G.574, E.628, H.660, Q.663, R.734 Chain D: T.562, R.565, R.654 15 PLIP interactions: 2 interactions with chain D, 13 interactions with chain C Salt bridges: D:R.565, D:R.654, C:R.470, C:R.470, C:H.660, C:R.734 Hydrogen bonds: C:R.470, C:R.470, C:T.527, C:S.529, C:N.531, C:G.574, C:E.628, C:E.628, C:Q.663 FBP.14: 17 residues within 4Å: Chain C: T.562, R.565, R.654 Chain D: A.409, R.470, G.497, F.498, T.527, I.528, S.529, N.531, M.572, G.574, E.628, H.660, Q.663, R.734 16 PLIP interactions: 14 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.470, D:R.470, D:T.527, D:T.527, D:S.529, D:N.531, D:G.574, D:E.628, D:E.628, D:Q.663 Salt bridges: D:R.470, D:R.470, D:H.660, D:R.734, C:R.565, C:R.654

4 x F6P: 6-O-phosphono-beta-D-fructofuranose(Post Translational Modification)

F6P.3: 10 residues within 4Å: Chain A: G.25, I.165, D.166, M.208, R.210, E.264, H.298, R.301 Chain B: R.201, R.292 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.166, A:E.264, A:R.301 Salt bridges: A:H.298, A:R.301, B:R.201, B:R.292 F6P.7: 10 residues within 4Å: Chain A: R.201, R.292 Chain B: G.25, I.165, D.166, M.208, R.210, E.264, H.298, R.301 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Salt bridges: A:R.201, A:R.292, B:H.298, B:R.301 Hydrogen bonds: B:D.166, B:E.264, B:R.301 F6P.11: 10 residues within 4Å: Chain C: G.25, I.165, D.166, M.208, R.210, E.264, H.298, R.301 Chain D: R.201, R.292 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain C Salt bridges: D:R.201, D:R.292, C:H.298, C:R.301 Hydrogen bonds: C:D.166, C:E.264, C:R.301 F6P.15: 10 residues within 4Å: Chain C: R.201, R.292 Chain D: G.25, I.165, D.166, M.208, R.210, E.264, H.298, R.301 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:D.166, D:E.264, D:R.301 Salt bridges: D:H.298, D:R.301, C:R.201, C:R.292

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

ADP.4: 16 residues within 4Å: Chain A: S.23, G.24, G.25, Y.55, R.88, C.89, F.92, T.93, R.98, G.118, D.119, G.120, S.121, T.123, G.124, I.127 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.25, A:C.89, A:C.89, A:T.93, A:G.118, A:G.118, A:D.119, A:G.120, A:S.121, A:S.121 Salt bridges: A:R.88 ADP.8: 16 residues within 4Å: Chain B: S.23, G.24, G.25, Y.55, R.88, C.89, F.92, T.93, R.98, G.118, D.119, G.120, S.121, T.123, G.124, I.127 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.25, B:C.89, B:C.89, B:T.93, B:G.118, B:D.119, B:D.119, B:G.120, B:S.121, B:S.121 Salt bridges: B:R.88 ADP.12: 16 residues within 4Å: Chain C: S.23, G.24, G.25, Y.55, R.88, C.89, F.92, T.93, R.98, G.118, D.119, G.120, S.121, T.123, G.124, I.127 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.25, C:C.89, C:C.89, C:T.93, C:G.118, C:G.118, C:D.119, C:G.120, C:S.121, C:S.121 Salt bridges: C:R.88 ADP.16: 16 residues within 4Å: Chain D: S.23, G.24, G.25, Y.55, R.88, C.89, F.92, T.93, R.98, G.118, D.119, G.120, S.121, T.123, G.124, I.127 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.25, D:C.89, D:C.89, D:T.93, D:G.118, D:D.119, D:D.119, D:G.120, D:S.121, D:S.121 Salt bridges: D:R.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Amara, N. et al., Selective activation of PFKL suppresses the phagocytic oxidative burst. Cell (2021)

Release Date

2022-01-26

Peptides

ATP-dependent 6-phosphofructokinase, liver type: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
E

D
F

ATP-dependent 6-phosphofructokinase, liver type