SMTL ID : 8w2g.1

Human liver phosphofructokinase-1 in the R-state conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x F6P: 6-O-phosphono-beta-D-fructofuranose

F6P.1: 12 residues within 4Å: Chain A: G.25, R.88, I.165, D.166, M.208, G.209, R.210, E.264, H.298, R.301 Chain C: R.201, R.292 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:D.166, A:D.166, A:G.209, A:E.264, A:R.301 Salt bridges: A:H.298, A:R.301, C:R.201, C:R.292 F6P.6: 12 residues within 4Å: Chain B: G.25, R.88, 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 B, 2 interactions with chain D Hydrogen bonds: B:D.166, B:D.166, B:G.209, B:E.264, B:R.301 Salt bridges: B:H.298, B:R.301, D:R.201, D:R.292 F6P.11: 12 residues within 4Å: Chain A: R.201, R.292 Chain C: 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 C, 2 interactions with chain A Hydrogen bonds: C:D.166, C:D.166, C:G.209, C:E.264, C:R.301 Salt bridges: C:H.298, C:R.301, A:R.201, A:R.292 F6P.16: 12 residues within 4Å: Chain B: R.201, R.292 Chain D: 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 D, 2 interactions with chain B Hydrogen bonds: D:D.166, D:D.166, D:G.209, D:E.264, D:R.301 Salt bridges: D:H.298, D:R.301, B:R.201, B:R.292

12 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.2: 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 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.25, A:R.88, A:C.89, A:C.89, A:G.118, A:D.119, A:G.120, A:S.121, 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, D.542, F.670, K.677, K.681, L.712 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: 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, E.236, W.382, Y.385, K.386, A.389, H.390, K.392 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:L.228, A:Y.385, A:H.390 Salt bridges: A:K.392, A:K.392 pi-Stacking: A:W.227, A:W.227, A:W.227 ADP.7: 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 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.25, B:R.88, B:C.89, B:C.89, B:G.118, B:D.119, B:G.120, B:S.121, 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, D.542, F.670, K.677, K.681, L.712 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.381, B:D.542 Salt bridges: B:K.677, B:K.677 pi-Stacking: B:F.308, B:F.308, B:F.537, B:F.670 ADP.9: 10 residues within 4Å: Chain B: D.226, W.227, L.228, E.236, W.382, Y.385, K.386, A.389, H.390, K.392 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:L.228, B:Y.385, B:H.390 Salt bridges: B:K.392, B:K.392 pi-Stacking: B:W.227, B:W.227, B:W.227 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 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.25, C:R.88, C:C.89, C:C.89, C:G.118, C:D.119, C:D.119, C:G.120, C:S.121, C:S.121 ADP.13: 14 residues within 4Å: Chain C: D.173, M.174, D.179, Y.214, F.308, G.340, N.341, S.377, N.381, D.542, F.670, K.677, K.681, 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.537, C:F.670 ADP.14: 10 residues within 4Å: Chain C: D.226, W.227, L.228, E.236, W.382, Y.385, K.386, A.389, H.390, K.392 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:L.228, C:Y.385, C:H.390 Salt bridges: C:K.392, C:K.392 pi-Stacking: C:W.227, C:W.227, C:W.227 ADP.17: 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 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:G.25, D:R.88, D:C.89, D:C.89, D:G.118, D:D.119, D:D.119, 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, D.542, F.670, K.677, K.681, L.712 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:N.381, D:D.542 Salt bridges: D:K.677, D:K.677 pi-Stacking: D:F.308, D:F.308, D:F.537, D:F.670 ADP.19: 10 residues within 4Å: Chain D: D.226, W.227, L.228, E.236, W.382, Y.385, K.386, A.389, H.390, K.392 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:L.228, D:Y.385, D:H.390 Salt bridges: D:K.392, D:K.392 pi-Stacking: D:W.227, D:W.227, D:W.227

4 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose

FBP.5: 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.573, G.574, E.628, H.660, Q.663, R.734 Chain C: R.565, R.654 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain C 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, C:R.565, C:R.654 FBP.10: 17 residues within 4Å: Chain B: A.409, R.470, G.497, 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 D: R.565, R.654 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain D 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:E.628, B:Q.663 Salt bridges: B:R.470, B:R.470, B:H.660, B:R.734, D:R.565, D:R.654 FBP.15: 16 residues within 4Å: Chain A: R.565, R.654 Chain C: 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: 14 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:R.470, C:R.470, C:T.527, C:S.529, C:S.529, C:N.531, C:G.573, C:G.574, C:E.628, C:Q.663 Salt bridges: C:R.470, C:R.470, C:H.660, C:R.734, A:R.565, A:R.654 FBP.20: 17 residues within 4Å: Chain B: 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.573, G.574, E.628, H.660, Q.663, R.734 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:R.470, D:R.470, D:T.527, D:S.529, D:S.529, D:N.531, D:G.573, 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, B:R.565, B:R.654

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

2024-09-11

Peptides

ATP-dependent 6-phosphofructokinase, liver type: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
B

D
C

ATP-dependent 6-phosphofructokinase, liver type

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