SMTL ID : 3f5m.1

Crystal Structure of ATP-Bound Phosphofructokinase from Trypanosoma brucei

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 18 residues within 4Å: Chain A: C.105, G.106, G.107, Y.139, R.173, G.174, P.175, G.197, G.198, D.199, G.200, T.201, R.203, G.204, K.226, S.341, N.343 Ligands: MG.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.107, A:G.174, A:G.198, A:G.198, A:G.200, A:T.201, A:S.341, A:S.341, A:N.343, A:N.343 Salt bridges: A:R.173, A:R.173, A:K.226, A:K.226 ATP.6: 18 residues within 4Å: Chain B: C.105, G.106, G.107, Y.139, R.173, G.174, P.175, G.197, G.198, D.199, G.200, T.201, R.203, G.204, K.226, S.341, N.343 Ligands: MG.7 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:G.107, B:G.174, B:G.198, B:G.198, B:G.200, B:T.201, B:T.201, B:S.341, B:S.341, B:N.343 Water bridges: B:D.199, B:N.343, B:R.383 Salt bridges: B:R.173, B:R.173, B:K.226 ATP.9: 17 residues within 4Å: Chain C: C.105, G.106, G.107, Y.139, R.173, G.174, P.175, G.197, G.198, D.199, G.200, T.201, R.203, G.204, K.226, S.341, N.343 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:G.107, C:S.172, C:G.174, C:G.198, C:G.200, C:T.201, C:S.341, C:S.341, C:N.343, C:N.343 Water bridges: C:D.199 Salt bridges: C:R.173, C:R.173, C:K.226, C:K.226 ATP.13: 18 residues within 4Å: Chain D: C.105, G.106, G.107, Y.139, R.173, G.174, P.175, G.197, G.198, D.199, G.200, T.201, R.203, G.204, K.226, S.341, N.343 Ligands: MG.14 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:G.107, D:G.174, D:G.198, D:G.198, D:G.200, D:T.201, D:T.201, D:S.341, D:S.341, D:N.343, D:N.343 Water bridges: D:S.172, D:S.172, D:D.199 Salt bridges: D:R.173, D:R.173, D:K.226

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: N.343 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: G.200, N.343 Ligands: ATP.6 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain D: N.343 Ligands: ATP.13 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: N.291, I.292, C.293, L.308, W.444, T.451, V.452 Ligands: NA.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.293, A:C.293, A:T.451 Water bridges: A:N.298 GOL.10: 8 residues within 4Å: Chain C: I.292, C.293, L.294, N.298, L.308, W.444, T.451 Ligands: NA.12 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:C.293, C:C.293, C:T.451 Water bridges: C:C.293, C:N.298

4 x NA: SODIUM ION(Non-functional Binders)

NA.4: 5 residues within 4Å: Chain A: R.448, T.451, V.452, D.453 Ligands: GOL.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.448 NA.5: 6 residues within 4Å: Chain A: A.259, V.260, A.262, R.317, S.318 Chain D: F.137 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.262, A:R.317 NA.8: 5 residues within 4Å: Chain B: V.260, A.262, R.317, S.318 Chain C: F.137 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Water bridges: C:R.136, B:R.317 Hydrogen bonds: B:R.317 NA.12: 5 residues within 4Å: Chain C: R.448, T.451, V.452, D.453 Ligands: GOL.10 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.453 Water bridges: C:T.451

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.11: 5 residues within 4Å: Chain B: K.374 Chain C: G.106, G.107, S.171, S.172 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.106, C:I.108 Salt bridges: C:R.173, B:K.374

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McNae, I.W. et al., The crystal structure of ATP-bound phosphofructokinase from Trypanosoma brucei reveals conformational transitions different from those of other phosphofructokinases. J.Mol.Biol. (2009)

Release Date

2008-11-25

Peptides

6-phospho-1-fructokinase (ATP-dependent phosphofructokinase): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

6-phospho-1-fructokinase (ATP-dependent phosphofructokinase)

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