SMTL ID : 8w2h.1

Human liver phosphofructokinase-1 in the T-state conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

FBP.1: 18 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: R.565, R.654 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.470, A:T.527, A:S.529, A:N.531, A:G.573, A:G.574, A:E.628, A:Q.663 Salt bridges: A:R.470, A:H.660, A:R.734, B:R.565, B:R.654 FBP.6: 18 residues within 4Å: Chain A: 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 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrogen bonds: 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 Salt bridges: B:R.470, B:H.660, B:R.734, A:R.565, A:R.654 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 14 PLIP interactions: 12 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, C:Q.663 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: 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, K.629, 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:S.529, D:N.531, D:G.573, D:G.574, D:E.628, D:Q.663 Salt bridges: D:R.470, D:H.660, D:R.734, C:R.565, C:R.654

12 x ATP: ADENOSINE-5'-TRIPHOSPHATE

ATP.2: 13 residues within 4Å: Chain A: T.193, T.194, Q.197, G.224, S.255, L.257, R.419, R.423, A.456, G.457, W.458, G.460, R.461 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.197, A:Q.197, A:S.255, A:G.457, A:G.460, 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:C.89, A:G.118, A:G.120, A:S.121, A:D.166 Salt bridges: A:R.88, A:R.88, A:R.88, A:R.301 ATP.4: 12 residues within 4Å: Chain A: A.225, D.226, W.227, L.228, E.236, F.242, R.246, W.382, Y.385, K.386, A.389, K.392 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:L.228, A:R.246, A:R.246, A:Y.385, A:K.386 Salt bridges: A:K.386, A:K.392, A:K.392, A:K.392 pi-Stacking: A:W.227, A:W.227, A:W.227 ATP.7: 13 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, W.458, G.460, R.461 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: 21 residues within 4Å: Chain B: 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.10 11 PLIP interactions: 11 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, B:R.88, B:R.301 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 12 PLIP interactions: 12 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, B:K.392 pi-Stacking: B:W.227, B:W.227, B:W.227 ATP.12: 13 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, W.458, G.460, R.461 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:Q.197, C:Q.197, C:S.255, C:G.457, C:G.460, C:R.461, C:R.461 Salt bridges: C:R.419, C:R.423 ATP.13: 21 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, D.166, R.301 Ligands: MG.15 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.25, C:C.89, C:C.89, C:G.118, C:G.120, C:S.121, 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 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:L.228, C:R.246, C:R.246, C:Y.385, C:K.386 Salt bridges: C:K.386, C:K.392, C:K.392, C:K.392 pi-Stacking: C:W.227, C:W.227, C:W.227 ATP.17: 13 residues within 4Å: Chain D: T.193, T.194, Q.197, G.224, S.255, L.257, R.419, R.423, A.456, G.457, W.458, G.460, R.461 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:Q.197, D:Q.197, D:S.255, D:G.457, D:G.460, D:R.461, D:R.461 Salt bridges: D:R.419, D:R.423 ATP.18: 21 residues within 4Å: Chain D: 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.20 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.25, D:C.89, D:C.89, D:G.118, D:G.120, D:S.121, D:D.166 Salt bridges: D:R.88, D:R.88, D:R.88, D:R.301 ATP.19: 12 residues within 4Å: Chain D: A.225, D.226, W.227, L.228, E.236, F.242, R.246, W.382, Y.385, K.386, A.389, K.392 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:L.228, D:R.246, D:R.246, D:Y.385, D:K.386 Salt bridges: D:K.386, D:K.392, D:K.392, D:K.392 pi-Stacking: D:W.227, D:W.227, D:W.227

4 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

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
B

C
C

D
D

ATP-dependent 6-phosphofructokinase, liver type

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