SMTL ID : 6sy7.1 (1 other biounit)

Structure of Trypanosome Brucei Phosphofructokinase in complex with AMP.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-tetramer

Ligands

4 x BNZ: BENZENE(Non-covalent)

BNZ.1: 7 residues within 4Å: Chain A: G.197, G.198, D.199, Q.202, T.227, L.232, A.430 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.199, A:Q.202, A:T.227, A:L.232 BNZ.5: 5 residues within 4Å: Chain B: G.198, D.199, T.227, L.232, A.430 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.199, B:T.227, B:L.232 BNZ.7: 6 residues within 4Å: Chain C: G.198, D.199, T.227, L.232, A.430, T.431 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:D.199, C:T.227, C:L.232, C:T.431 BNZ.11: 5 residues within 4Å: Chain D: G.198, D.199, T.227, D.231, L.232 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:D.199, D:L.232

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: I.292, C.293, L.294, N.298, W.444, T.451 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:C.293, A:N.298, A:T.451, A:T.451 Water bridges: A:N.298, A:R.448 GOL.6: 5 residues within 4Å: Chain B: I.292, C.293, N.298, W.444, T.451 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:C.293, B:N.298, B:T.451, B:T.451 GOL.8: 8 residues within 4Å: Chain C: N.291, I.292, C.293, L.294, N.298, I.300, W.444, T.451 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.291, C:C.293, C:N.298 Water bridges: C:C.293, C:N.298 GOL.12: 6 residues within 4Å: Chain D: I.292, C.293, L.294, N.298, W.444, T.451 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:C.293, D:N.298, D:T.451, D:T.451 Water bridges: D:N.298, D:R.448

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 15 residues within 4Å: Chain A: A.288, Q.289, A.290, N.291, R.312, I.450 Chain B: R.117, S.118, L.121, T.122, N.125, R.155, T.159, A.396, T.400 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:R.117, B:R.117, B:T.122, B:N.125, B:T.400, A:A.290, A:N.291, A:R.312, A:R.312, A:S.316 Salt bridges: B:R.155, A:R.312 AMP.4: 16 residues within 4Å: Chain A: R.117, S.118, L.121, T.122, N.125, R.155, T.159, A.396, T.400 Chain B: A.288, Q.289, A.290, N.291, R.312, E.449, I.450 14 PLIP interactions: 7 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:R.117, A:R.117, A:T.122, A:N.125, A:T.400, A:T.400, B:A.290, B:N.291, B:R.312, B:R.312, B:S.316, B:Q.446 Salt bridges: A:R.155, B:R.312 AMP.9: 15 residues within 4Å: Chain C: A.288, Q.289, A.290, N.291, R.312, I.450 Chain D: R.117, S.118, L.121, T.122, N.125, R.155, T.159, A.396, T.400 11 PLIP interactions: 6 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:A.290, C:N.291, C:R.312, C:R.312, D:R.117, D:R.117, D:N.125, D:T.400 Water bridges: C:S.316 Salt bridges: C:R.312, D:R.155 AMP.10: 14 residues within 4Å: Chain C: R.117, S.118, L.121, T.122, N.125, R.155, T.159, T.400 Chain D: A.288, Q.289, A.290, N.291, R.312, I.450 11 PLIP interactions: 5 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:R.117, C:R.117, C:N.125, C:T.400, D:A.290, D:N.291, D:R.312, D:R.312 Salt bridges: C:R.155, D:R.312 Water bridges: D:S.316

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fernandes, P.M. et al., Kinetic and structural studies of Trypanosoma and Leishmania phosphofructokinases show evolutionary divergence and identify AMP as a switch regulating glycolysis versus gluconeogenesis. Febs J. (2020)

Release Date

2019-12-25

Peptides

ATP-dependent 6-phosphofructokinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

ATP-dependent 6-phosphofructokinase

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