SMTL ID : 8w2j.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

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

FBP.1: 19 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, K.629, H.660, Q.663, R.734 Chain B: K.563, R.565, R.654 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.470, A:T.527, A:T.527, A:S.529, A:N.531, A:G.573, A:G.574, A:E.628 Salt bridges: A:R.470, A:R.470, A:H.660, A:R.734, B:R.565, B:R.654 FBP.6: 19 residues within 4Å: Chain A: K.563, 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.573, G.574, E.628, K.629, H.660, Q.663, R.734 12 PLIP interactions: 2 interactions with chain A, 10 interactions with chain B Salt bridges: A:R.565, A:R.654, B:R.470, B:H.660, B:R.734 Hydrogen bonds: B:R.470, B:T.527, B:S.529, B:N.531, B:G.573, B:G.574, B:E.628 FBP.11: 18 residues within 4Å: Chain C: A.409, R.470, G.497, F.498, T.527, I.528, S.529, N.531, M.572, G.573, G.574, E.628, K.629, H.660, Q.663, R.734 Chain D: R.565, R.654 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.470, C:T.527, C:T.527, C:S.529, C:N.531, C:G.573, C:G.574, C:E.628 Salt bridges: C:R.470, C:H.660, C:R.734, D:R.565, D:R.654 FBP.16: 18 residues within 4Å: Chain C: K.563, 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 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.470, D:T.527, D:T.527, D:S.529, D:N.531, D:G.573, D:G.574, D:E.628 Salt bridges: D:R.470, D:H.660, D:R.734, C:R.565, C:R.654 FBP.21: 18 residues within 4Å: Chain E: A.409, R.470, G.497, F.498, T.527, I.528, S.529, N.531, M.572, G.573, G.574, E.628, K.629, H.660, Q.663, R.734 Chain F: R.565, R.654 13 PLIP interactions: 11 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:R.470, E:T.527, E:T.527, E:S.529, E:N.531, E:G.573, E:G.574, E:E.628 Salt bridges: E:R.470, E:H.660, E:R.734, F:R.565, F:R.654 FBP.26: 18 residues within 4Å: Chain E: R.565, R.654 Chain F: A.409, R.470, G.497, F.498, T.527, I.528, S.529, N.531, M.572, G.573, G.574, E.628, K.629, H.660, Q.663, R.734 13 PLIP interactions: 2 interactions with chain E, 11 interactions with chain F Salt bridges: E:R.565, E:R.654, F:R.470, F:H.660, F:R.734 Hydrogen bonds: F:R.470, F:T.527, F:T.527, F:S.529, F:N.531, F:G.573, F:G.574, F:E.628 FBP.31: 18 residues within 4Å: Chain G: A.409, R.470, G.497, F.498, T.527, I.528, S.529, N.531, M.572, G.573, G.574, E.628, K.629, H.660, Q.663, R.734 Chain H: R.565, R.654 12 PLIP interactions: 10 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:R.470, G:T.527, G:S.529, G:N.531, G:G.573, G:G.574, G:E.628 Salt bridges: G:R.470, G:H.660, G:R.734, H:R.565, H:R.654 FBP.36: 18 residues within 4Å: Chain G: K.563, R.565, R.654 Chain H: A.409, R.470, G.497, T.527, I.528, S.529, N.531, M.572, G.573, G.574, E.628, K.629, H.660, Q.663, R.734 13 PLIP interactions: 11 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:R.470, H:T.527, H:T.527, H:S.529, H:N.531, H:G.573, H:G.574, H:E.628 Salt bridges: H:R.470, H:H.660, H:R.734, G:R.565, G:R.654

24 x ATP: ADENOSINE-5'-TRIPHOSPHATE

ATP.2: 12 residues within 4Å: Chain A: T.193, T.194, Q.197, G.224, S.255, R.256, R.419, R.423, A.456, G.457, G.460, R.461 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.197, A:Q.197, A:S.255, A:G.457, A:R.461, A:R.461 Salt bridges: A:R.419, A:R.423 ATP.3: 21 residues within 4Å: Chain A: S.23, G.24, G.25, Y.55, R.88, C.89, K.90, F.92, T.93, R.98, G.118, D.119, G.120, S.121, T.123, G.124, I.127, S.164, D.166, R.301 Ligands: MG.5 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.25, A:C.89, A:G.118, A:D.119, A:D.119, A:G.120, A:S.121, A:D.166 Salt bridges: A:R.88, A:R.88, A:R.88 ATP.4: 11 residues within 4Å: Chain A: D.226, W.227, L.228, E.236, F.242, R.246, W.382, Y.385, K.386, A.389, K.392 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.226, A:L.228, A:R.246, A:R.246, A:K.386 Salt bridges: A:K.386, A:K.392, A:K.392 pi-Stacking: A:W.227 ATP.7: 14 residues within 4Å: Chain B: T.193, T.194, Q.197, G.224, S.255, L.257, R.419, R.423, A.456, G.457, L.459, G.460, R.461, G.462 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Q.197, B:Q.197, B:S.255, B:G.457, B:G.460, B:R.461, B:R.461 Salt bridges: B:R.419, B:R.423 ATP.8: 22 residues within 4Å: Chain B: S.23, G.24, G.25, Y.55, A.87, R.88, C.89, K.90, F.92, T.93, R.98, G.118, D.119, G.120, S.121, T.123, G.124, I.127, S.164, D.166, R.301 Ligands: MG.10 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.25, B:C.89, B:C.89, B:G.118, B:G.120, B:S.121, B:D.166 Salt bridges: B:R.88, B:R.88 ATP.9: 12 residues within 4Å: Chain B: A.225, D.226, W.227, L.228, E.236, F.242, R.246, W.382, Y.385, K.386, A.389, K.392 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:L.228, B:R.246, B:R.246, B:Y.385, B:K.386 Salt bridges: B:K.386, B:K.392, B:K.392 pi-Stacking: B:W.227, B:W.227, B:W.227 ATP.12: 12 residues within 4Å: Chain C: T.193, T.194, Q.197, G.224, S.255, L.257, R.419, R.423, A.456, G.457, G.460, R.461 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.197, C:S.255, C:G.457, C:R.461 Salt bridges: C:R.419, C:R.423 ATP.13: 22 residues within 4Å: Chain C: S.23, G.24, G.25, Y.55, R.88, C.89, K.90, F.92, T.93, R.98, G.118, D.119, G.120, S.121, T.123, G.124, I.127, S.164, I.165, D.166, R.301 Ligands: MG.15 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:G.25, C:C.89, C:C.89, C:C.89, C:G.118, C:D.119, C:G.120, C:S.121, C:D.166, C:D.166, C:R.301 Salt bridges: C:R.88, C:R.88, C:R.88 ATP.14: 12 residues within 4Å: Chain C: A.225, D.226, W.227, L.228, E.236, F.242, R.246, W.382, Y.385, K.386, A.389, K.392 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:L.228, C:R.246, C:R.246, C:Y.385 Salt bridges: C:K.386, C:K.392, C:K.392 pi-Stacking: C:W.227, C:W.227, C:W.227 pi-Cation interactions: C:K.386 ATP.17: 14 residues within 4Å: Chain D: T.193, T.194, Q.197, G.224, S.255, R.256, L.257, R.419, R.423, A.456, G.457, L.459, G.460, R.461 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:Q.197, D:Q.197, D:S.255, D:L.257, D:G.457, D:R.461, D:R.461 Salt bridges: D:R.419, D:R.423 ATP.18: 22 residues within 4Å: Chain D: S.23, G.24, G.25, Y.55, A.87, R.88, C.89, K.90, F.92, T.93, R.98, G.118, D.119, G.120, S.121, T.123, G.124, I.127, S.164, D.166, R.301 Ligands: MG.20 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:G.25, D:C.89, D:C.89, D:G.118, D:D.119, D:G.120, D:S.121 Salt bridges: D:R.88, D:R.88, D:R.88 ATP.19: 11 residues within 4Å: Chain D: D.226, W.227, L.228, E.236, F.242, R.246, W.382, Y.385, K.386, A.389, K.392 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:L.228, D:E.236, D:R.246, D:R.246, D:Y.385 Salt bridges: D:K.386, D:K.392, D:K.392 pi-Stacking: D:W.227 ATP.22: 13 residues within 4Å: Chain E: T.193, T.194, Q.197, G.224, S.255, R.256, L.257, R.419, R.423, A.456, G.457, G.460, R.461 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:Q.197, E:Q.197, E:S.255, E:L.257, E:G.457, E:R.461, E:R.461 Salt bridges: E:R.419, E:R.423 ATP.23: 22 residues within 4Å: Chain E: S.23, G.24, G.25, Y.55, A.87, R.88, C.89, K.90, F.92, T.93, R.98, G.118, D.119, G.120, S.121, T.123, G.124, I.127, S.164, D.166, R.301 Ligands: MG.25 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:G.25, E:C.89, E:C.89, E:G.118, E:D.119, E:G.120, E:S.121 Salt bridges: E:R.88, E:R.88, E:R.88 ATP.24: 11 residues within 4Å: Chain E: D.226, W.227, L.228, E.236, F.242, R.246, W.382, Y.385, K.386, A.389, K.392 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:L.228, E:E.236, E:R.246, E:R.246, E:Y.385 Salt bridges: E:K.386, E:K.392, E:K.392 pi-Stacking: E:W.227 ATP.27: 12 residues within 4Å: Chain F: T.193, T.194, Q.197, G.224, S.255, L.257, R.419, R.423, A.456, G.457, G.460, R.461 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:Q.197, F:S.255, F:G.457, F:G.460, F:R.461 Salt bridges: F:R.419, F:R.423 ATP.28: 22 residues within 4Å: Chain F: S.23, G.24, G.25, Y.55, R.88, C.89, K.90, F.92, T.93, R.98, G.118, D.119, G.120, S.121, T.123, G.124, I.127, S.164, I.165, D.166, R.301 Ligands: MG.30 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:G.25, F:R.88, F:C.89, F:C.89, F:C.89, F:G.118, F:D.119, F:G.120, F:S.121, F:D.166, F:D.166, F:R.301 Salt bridges: F:R.88, F:R.88 ATP.29: 12 residues within 4Å: Chain F: A.225, D.226, W.227, L.228, E.236, F.242, R.246, W.382, Y.385, K.386, A.389, K.392 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:L.228, F:R.246, F:R.246, F:Y.385 Salt bridges: F:K.386, F:K.392, F:K.392 pi-Stacking: F:W.227, F:W.227, F:W.227 pi-Cation interactions: F:K.386 ATP.32: 14 residues within 4Å: Chain G: T.193, T.194, Q.197, G.224, S.255, L.257, R.419, R.423, A.456, G.457, L.459, G.460, R.461, G.462 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:Q.197, G:Q.197, G:S.255, G:G.457, G:G.460, G:R.461, G:R.461 Salt bridges: G:R.419, G:R.423 ATP.33: 22 residues within 4Å: Chain G: S.23, G.24, G.25, Y.55, A.87, R.88, C.89, K.90, F.92, T.93, R.98, G.118, D.119, G.120, S.121, T.123, G.124, I.127, S.164, D.166, R.301 Ligands: MG.35 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:G.25, G:C.89, G:C.89, G:G.118, G:G.120, G:S.121, G:D.166, G:R.301 Salt bridges: G:R.88, G:R.88, G:R.88 ATP.34: 12 residues within 4Å: Chain G: A.225, D.226, W.227, L.228, E.236, F.242, R.246, W.382, Y.385, K.386, A.389, K.392 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:L.228, G:R.246, G:R.246, G:Y.385, G:K.386 Salt bridges: G:K.386, G:K.392, G:K.392 pi-Stacking: G:W.227, G:W.227, G:W.227 ATP.37: 13 residues within 4Å: Chain H: T.193, T.194, Q.197, G.224, S.255, R.256, L.257, R.419, R.423, A.456, G.457, G.460, R.461 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:Q.197, H:Q.197, H:S.255, H:G.457, H:G.460, H:R.461, H:R.461 Salt bridges: H:R.419, H:R.423 ATP.38: 22 residues within 4Å: Chain H: S.23, G.24, G.25, Y.55, A.87, R.88, C.89, K.90, F.92, T.93, R.98, G.118, D.119, G.120, S.121, T.123, G.124, I.127, S.164, D.166, R.301 Ligands: MG.40 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:G.25, H:C.89, H:T.93, H:G.118, H:D.119, H:D.119, H:G.120, H:S.121, H:D.166 Salt bridges: H:R.88, H:R.88, H:R.88 ATP.39: 11 residues within 4Å: Chain H: D.226, W.227, L.228, E.236, F.242, R.246, W.382, Y.385, K.386, A.389, K.392 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:D.226, H:L.228, H:R.246, H:R.246, H:K.386 Salt bridges: H:K.386, H:K.392, H:K.392 pi-Stacking: H:W.227

8 x MG: MAGNESIUM ION

MG.5: 4 residues within 4Å: Chain A: G.118, D.119, G.120 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.119 MG.10: 4 residues within 4Å: Chain B: G.118, D.119, G.120 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.119 MG.15: 4 residues within 4Å: Chain C: G.118, D.119, G.120 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.119 MG.20: 4 residues within 4Å: Chain D: G.118, D.119, G.120 Ligands: ATP.18 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.119 MG.25: 4 residues within 4Å: Chain E: G.118, D.119, G.120 Ligands: ATP.23 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.119 MG.30: 4 residues within 4Å: Chain F: G.118, D.119, G.120 Ligands: ATP.28 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.119 MG.35: 4 residues within 4Å: Chain G: G.118, D.119, G.120 Ligands: ATP.33 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.119 MG.40: 4 residues within 4Å: Chain H: G.118, D.119, G.120 Ligands: ATP.38 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.119

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: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

E
A

F
B

G
C

H
D

ATP-dependent 6-phosphofructokinase, liver type

Related Entries With Identical Sequence