SMTL ID : 8w2i.1

Human liver phosphofructokinase-1 filament in the R-state conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

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

F6P.1: 12 residues within 4Å: Chain A: R.88, S.164, I.165, D.166, M.208, G.209, R.210, E.264, H.298, R.301 Chain B: R.201, R.292 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.164, A:D.166, A:D.166, A:G.209, A:E.264, A:R.301 Salt bridges: A:H.298, A:R.301, B:R.201, B:R.292 F6P.6: 11 residues within 4Å: Chain A: R.201, R.292 Chain B: G.25, I.165, D.166, M.208, G.209, R.210, E.264, H.298, R.301 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain B Salt bridges: A:R.201, A:R.292, B:H.298, B:R.301 Hydrogen bonds: B:D.166, B:G.209, B:R.210, B:E.264, B:R.301 F6P.15: 13 residues within 4Å: Chain C: G.25, R.88, S.164, I.165, D.166, M.208, G.209, R.210, E.264, H.298, R.301 Chain D: R.201, R.292 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:S.164, C:D.166, C:D.166, C:G.209, C:R.301 Salt bridges: C:H.298, C:R.301, D:R.201, D:R.292 F6P.16: 11 residues within 4Å: Chain C: R.201, R.292 Chain D: R.88, I.165, D.166, M.208, G.209, R.210, E.264, H.298, R.301 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.88, D:D.166, D:E.264, D:R.301 Salt bridges: D:H.298, D:R.301, C:R.201, C:R.292 F6P.21: 11 residues within 4Å: Chain E: R.88, I.165, D.166, M.208, G.209, R.210, E.264, H.298, R.301 Chain F: R.201, R.292 8 PLIP interactions: 6 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:R.88, E:D.166, E:E.264, E:R.301 Salt bridges: E:H.298, E:R.301, F:R.201, F:R.292 F6P.26: 10 residues within 4Å: Chain E: R.201, R.292 Chain F: R.88, D.166, M.208, G.209, R.210, E.264, H.298, R.301 7 PLIP interactions: 2 interactions with chain E, 5 interactions with chain F Salt bridges: E:R.201, E:R.292, F:H.298, F:R.301 Hydrogen bonds: F:D.166, F:G.209, F:R.301 F6P.31: 11 residues within 4Å: Chain G: G.25, I.165, D.166, M.208, G.209, R.210, E.264, H.298, R.301 Chain H: R.201, R.292 9 PLIP interactions: 7 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:D.166, G:G.209, G:R.210, G:E.264, G:R.301 Salt bridges: G:H.298, G:R.301, H:R.201, H:R.292 F6P.36: 12 residues within 4Å: Chain G: R.201, R.292 Chain H: G.25, R.88, I.165, D.166, M.208, G.209, R.210, E.264, H.298, R.301 9 PLIP interactions: 7 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:D.166, H:G.209, H:R.210, H:E.264, H:R.301 Salt bridges: H:H.298, H:R.301, G:R.201, G:R.292

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

ADP.2: 15 residues within 4Å: Chain A: S.23, G.24, G.25, Y.55, R.88, C.89, F.92, T.93, G.118, D.119, G.120, S.121, T.123, G.124, I.127 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.23, A:G.25, A:R.88, A:C.89, A:C.89, A:G.118, A:D.119, A:D.119, A:G.120, A:S.121 ADP.3: 14 residues within 4Å: Chain A: D.173, M.174, D.179, Y.214, F.308, G.340, N.341, S.377, N.381, F.537, D.542, F.670, K.677, L.712 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.179, A:N.381, A:D.542 Salt bridges: A:K.677, A:K.677 pi-Stacking: A:F.308, A:F.308, A:F.537, A:F.670 ADP.4: 10 residues within 4Å: Chain A: D.226, W.227, L.228, P.235, E.236, Y.385, K.386, A.389, H.390, K.392 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:L.228, A:Y.385, A:Y.385, A:H.390 Salt bridges: A:K.392, A:K.392 pi-Stacking: A:W.227 ADP.7: 13 residues within 4Å: Chain B: G.24, G.25, Y.55, R.88, C.89, F.92, T.93, G.118, D.119, G.120, S.121, G.124, I.127 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.25, B:C.89, B:G.118, B:D.119, B:G.120, B:S.121 ADP.8: 14 residues within 4Å: Chain B: D.173, M.174, D.179, Y.214, F.308, G.340, N.341, S.377, N.381, F.537, D.542, F.670, K.677, L.712 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.179, B:Y.214, B:N.381 Salt bridges: B:K.677, B:K.677 pi-Stacking: B:F.308, B:F.308, B:F.537, B:F.670 ADP.9: 11 residues within 4Å: Chain B: D.226, W.227, L.228, E.236, F.242, R.246, W.382, Y.385, K.386, A.389, H.390 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.226, B:L.228, B:H.390 pi-Stacking: B:W.227, B:W.227 ADP.11: 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 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:R.88, C:C.89, C:C.89, C:G.118, C:G.118, C:D.119, C:G.120, C:S.121, C:S.121 ADP.12: 12 residues within 4Å: Chain C: D.173, M.174, D.179, Y.214, F.308, S.377, F.378, N.381, D.542, F.670, K.677, L.712 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:N.381, C:D.542 Salt bridges: C:K.677, C:K.677 pi-Stacking: C:F.308, C:F.308, C:F.670, C:F.670 ADP.13: 11 residues within 4Å: Chain C: D.226, W.227, L.228, E.236, F.242, W.382, Y.385, K.386, A.389, H.390, K.392 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:L.228, C:Y.385, C:Y.385 Salt bridges: C:K.392, C:K.392 pi-Stacking: C:W.227, C:W.227 ADP.17: 15 residues within 4Å: Chain D: S.23, G.24, G.25, Y.55, R.88, C.89, F.92, T.93, G.118, D.119, G.120, S.121, T.123, G.124, I.127 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:S.23, D:R.88, D:C.89, D:G.118, D:G.118, D:D.119, D:G.120, D:G.120, D:S.121, D:S.121 ADP.18: 14 residues within 4Å: Chain D: D.173, M.174, D.179, Y.214, F.308, G.340, N.341, S.377, N.381, F.537, D.542, F.670, K.677, L.712 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:D.179, D:N.341, D:N.381 Salt bridges: D:K.677, D:K.677 pi-Stacking: D:F.308, D:F.670 ADP.19: 10 residues within 4Å: Chain D: D.226, W.227, L.228, P.235, W.382, Y.385, K.386, A.389, H.390, K.392 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:L.228, D:H.390 Salt bridges: D:K.392, D:K.392 pi-Stacking: D:W.227, D:W.227, D:W.227 ADP.22: 15 residues within 4Å: Chain E: S.23, G.24, G.25, Y.55, R.88, C.89, F.92, T.93, G.118, D.119, G.120, S.121, T.123, G.124, I.127 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:S.23, E:R.88, E:C.89, E:G.118, E:G.118, E:G.120, E:G.120, E:S.121, E:S.121 ADP.23: 14 residues within 4Å: Chain E: D.173, M.174, D.179, Y.214, F.308, G.340, N.341, S.377, N.381, F.537, D.542, F.670, K.677, L.712 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:N.341, E:N.381, E:D.542 Salt bridges: E:K.677, E:K.677 pi-Stacking: E:F.308, E:F.308, E:F.670 ADP.24: 11 residues within 4Å: Chain E: D.226, W.227, L.228, E.236, F.242, W.382, Y.385, K.386, A.389, H.390, K.392 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:L.228, E:E.236, E:Y.385 Salt bridges: E:K.392, E:K.392 pi-Stacking: E:W.227, E:W.227, E:W.227 ADP.27: 15 residues within 4Å: Chain F: S.23, G.24, G.25, Y.55, R.88, C.89, F.92, T.93, G.118, D.119, G.120, S.121, T.123, G.124, I.127 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:R.88, F:C.89, F:C.89, F:G.118, F:G.118, F:D.119, F:D.119, F:G.120, F:S.121, F:S.121 ADP.28: 12 residues within 4Å: Chain F: D.173, M.174, D.179, Y.214, F.308, S.377, N.381, D.542, F.670, K.677, K.681, L.712 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:N.381, F:D.542 Salt bridges: F:K.677, F:K.677 pi-Stacking: F:F.308, F:F.308, F:F.670, F:F.670 ADP.29: 11 residues within 4Å: Chain F: D.226, W.227, L.228, E.236, F.242, W.382, Y.385, K.386, A.389, H.390, K.392 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:L.228, F:Y.385, F:Y.385, F:H.390 Salt bridges: F:K.392, F:K.392 pi-Stacking: F:W.227 ADP.32: 13 residues within 4Å: Chain G: G.24, G.25, Y.55, R.88, C.89, F.92, T.93, G.118, D.119, G.120, S.121, G.124, I.127 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:G.25, G:C.89, G:G.118, G:D.119, G:G.120, G:S.121 ADP.33: 14 residues within 4Å: Chain G: D.173, M.174, D.179, Y.214, F.308, G.340, N.341, S.377, N.381, F.537, D.542, F.670, K.677, L.712 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:D.179, G:Y.214, G:N.381 Salt bridges: G:K.677, G:K.677 pi-Stacking: G:F.308, G:F.308, G:F.537, G:F.670 ADP.34: 10 residues within 4Å: Chain G: D.226, W.227, L.228, E.236, F.242, W.382, Y.385, K.386, A.389, H.390 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:D.226, G:L.228, G:H.390 pi-Stacking: G:W.227 ADP.37: 15 residues within 4Å: Chain H: S.23, G.24, G.25, Y.55, R.88, C.89, F.92, T.93, G.118, D.119, G.120, S.121, T.123, G.124, I.127 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:S.23, H:G.25, H:R.88, H:C.89, H:C.89, H:D.119, H:D.119, H:G.120, H:S.121 ADP.38: 14 residues within 4Å: Chain H: D.173, M.174, D.179, Y.214, F.308, G.340, N.341, S.377, N.381, F.537, D.542, F.670, K.677, L.712 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:D.179, H:N.381 Salt bridges: H:K.677, H:K.677 pi-Stacking: H:F.308, H:F.308, H:F.537, H:F.670 ADP.39: 10 residues within 4Å: Chain H: D.226, W.227, L.228, P.235, E.236, Y.385, K.386, A.389, H.390, K.392 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:L.228, H:Y.385, H:Y.385, H:H.390 Salt bridges: H:K.386, H:K.392, H:K.392 pi-Stacking: H:W.227

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

FBP.5: 16 residues within 4Å: Chain A: A.409, R.470, F.498, T.527, I.528, S.529, N.531, M.572, G.573, G.574, E.628, H.660, Q.663, R.734 Chain B: R.565, R.654 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.470, A:R.470, A:T.527, A:T.527, A:S.529, A:N.531, A:G.573, A:G.574, A:E.628, A:E.628, A:Q.663 Salt bridges: A:R.470, A:R.470, A:H.660, A:R.734, B:R.565, B:R.654 FBP.10: 16 residues within 4Å: Chain A: R.565, R.654 Chain B: A.409, R.470, F.498, T.527, I.528, S.529, N.531, M.572, G.573, G.574, E.628, H.660, Q.663, R.734 16 PLIP interactions: 2 interactions with chain A, 14 interactions with chain B Salt bridges: A:R.565, A:R.654, B:R.470, B:R.470, B:H.660, B:R.734 Hydrogen bonds: B:R.470, B:R.470, B:T.527, B:T.527, B:S.529, B:N.531, B:G.573, B:G.574, B:E.628, B:Q.663 FBP.14: 15 residues within 4Å: Chain C: A.409, R.470, F.498, T.527, I.528, S.529, N.531, M.572, G.573, G.574, H.660, Q.663, R.734 Chain D: 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:T.527, C:S.529, C:N.531, C:G.573, C:G.574, C:Q.663 FBP.20: 16 residues within 4Å: Chain C: R.565, R.654 Chain D: A.409, R.470, F.498, E.499, T.527, I.528, S.529, N.531, M.572, G.573, G.574, H.660, Q.663, R.734 13 PLIP interactions: 2 interactions with chain C, 11 interactions with chain D Hydrogen bonds: C:R.565, D:T.527, D:T.527, D:S.529, D:N.531, D:G.573, D:G.574, D:Q.663 Salt bridges: C:R.654, D:R.470, D:R.470, D:H.660, D:R.734 FBP.25: 16 residues within 4Å: Chain E: A.409, R.470, F.498, E.499, T.527, I.528, S.529, N.531, M.572, G.573, G.574, H.660, Q.663, R.734 Chain F: R.565, R.654 15 PLIP interactions: 13 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:R.470, E:R.470, E:T.527, E:T.527, E:S.529, E:N.531, E:G.573, E:G.574, E:Q.663, F:R.565 Salt bridges: E:R.470, E:R.470, E:H.660, E:R.734, F:R.654 FBP.30: 15 residues within 4Å: Chain E: R.565, R.654 Chain F: A.409, R.470, F.498, T.527, I.528, S.529, N.531, M.572, G.573, G.574, H.660, Q.663, R.734 15 PLIP interactions: 13 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:R.470, F:R.470, F:T.527, F:T.527, F:S.529, F:N.531, F:G.573, F:G.574, F:Q.663 Salt bridges: F:R.470, F:R.470, F:H.660, F:R.734, E:R.565, E:R.654 FBP.35: 16 residues within 4Å: Chain G: A.409, R.470, F.498, T.527, I.528, S.529, N.531, M.572, G.573, G.574, E.628, H.660, Q.663, R.734 Chain H: R.565, R.654 17 PLIP interactions: 15 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:R.470, G:R.470, G:T.527, G:T.527, G:S.529, G:N.531, G:G.573, G:G.574, G:E.628, G:E.628, G:Q.663 Salt bridges: G:R.470, G:R.470, G:H.660, G:R.734, H:R.565, H:R.654 FBP.40: 17 residues within 4Å: Chain G: R.565, R.654 Chain H: A.409, R.470, F.498, E.499, T.527, I.528, S.529, N.531, M.572, G.573, G.574, E.628, H.660, Q.663, R.734 17 PLIP interactions: 2 interactions with chain G, 15 interactions with chain H Salt bridges: G:R.565, G:R.654, H:R.470, H:R.470, H:H.660, H:R.734 Hydrogen bonds: H:R.470, H:R.470, H:T.527, H:T.527, H:S.529, H:N.531, H:G.573, H:G.574, H:E.628, H:E.628, H:Q.663

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lynch, E.M. et al., Structural basis for allosteric regulation of human phosphofructokinase-1. Nat Commun (2024)

Release Date

2025-01-29

Peptides

ATP-dependent 6-phosphofructokinase, liver type: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

ATP-dependent 6-phosphofructokinase, liver type

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