SMTL ID : 7tff.1

Crystal structure of human platelet phosphofructokinase-1 mutant- D564N

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.60 Å

Oligo State

homo-tetramer

Ligands

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 7 residues within 4Å: Chain A: G.261, D.263, K.292, R.458, R.462, G.495, G.496 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.263, A:G.496 Salt bridges: A:K.292, A:R.458, A:R.462 PO4.2: 4 residues within 4Å: Chain A: R.509, H.699 Chain B: R.604, R.693 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.604, B:R.693, A:R.509, A:H.699 PO4.7: 7 residues within 4Å: Chain B: R.72, R.76, S.111, S.112, K.595, G.627, R.660 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.112, B:G.627, B:G.627 Salt bridges: B:R.72, B:R.76, B:K.595, B:R.660 PO4.8: 8 residues within 4Å: Chain B: C.260, G.261, K.292, R.458, R.462, G.495, G.496, T.498 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.496, B:T.498 Salt bridges: B:K.292, B:R.458, B:R.462 PO4.11: 8 residues within 4Å: Chain C: R.72, R.76, V.110, S.111, S.112, K.595, G.627, R.660 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:V.110, C:S.112, C:G.627 Salt bridges: C:R.72, C:R.76, C:K.595, C:R.660 PO4.12: 7 residues within 4Å: Chain C: G.261, K.292, R.458, R.462, V.494, G.495, G.496 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:V.494, C:G.496 Salt bridges: C:K.292, C:R.458, C:R.462 PO4.17: 5 residues within 4Å: Chain C: R.604, R.693 Chain D: A.448, R.509, H.699 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Salt bridges: D:R.509, D:H.699, C:R.604, C:R.693 PO4.18: 7 residues within 4Å: Chain D: G.261, K.292, R.458, R.462, V.494, G.495, G.496 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.496 Salt bridges: D:K.292, D:R.458, D:R.462

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

SO4.3: 4 residues within 4Å: Chain A: R.604, R.693 Chain B: R.509, H.699 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.604, A:R.693, B:R.509, B:H.699 SO4.4: 7 residues within 4Å: Chain A: R.72, R.76, S.111, K.595, G.627, I.658, R.660 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.76, A:K.595, A:R.660 SO4.5: 3 residues within 4Å: Chain A: K.483, Q.485 Chain B: R.603 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.483, B:R.603 SO4.6: 3 residues within 4Å: Chain A: M.523, S.527, I.528 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.527 SO4.9: 5 residues within 4Å: Chain B: R.509, E.538, T.566, S.568, N.570 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.538, B:T.566, B:S.568, B:N.570, B:N.570 Salt bridges: B:R.509 SO4.10: 5 residues within 4Å: Chain B: N.163, K.167, P.369, A.370, M.386 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.163, B:A.370 Salt bridges: B:K.167 SO4.13: 4 residues within 4Å: Chain C: A.448, R.509, H.699 Chain D: R.604 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Salt bridges: D:R.604, D:R.693, C:R.509, C:H.699 SO4.14: 7 residues within 4Å: Chain C: R.509, E.538, T.566, S.568, N.570, G.612, G.613 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.538, C:T.566, C:S.568, C:S.568, C:N.570 Salt bridges: C:R.509 SO4.15: 5 residues within 4Å: Chain C: A.162, N.163, P.369, L.385, M.386 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.385 SO4.16: 5 residues within 4Å: Chain C: F.206, C.207, C.388, T.392, Q.393 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.392, C:Q.393 SO4.19: 8 residues within 4Å: Chain D: R.72, R.76, S.111, K.595, G.627, K.653, I.658, R.660 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.72, D:S.111, D:S.111 Salt bridges: D:R.76, D:K.595, D:K.653, D:R.660 SO4.20: 5 residues within 4Å: Chain D: R.509, E.538, T.566, S.568, N.570 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.568, D:N.570 Salt bridges: D:R.509 SO4.21: 5 residues within 4Å: Chain D: I.633, F.634, E.636, P.637, C.669 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:F.634

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Voronkova, M.A. et al., Cancer-associated somatic mutations in human phosphofructokinase-1 reveal a critical electrostatic interaction for allosteric regulation of enzyme activity. Biochem.J. (2023)

Release Date

2023-07-12

Peptides

ATP-dependent 6-phosphofructokinase, platelet type: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

ATP-dependent 6-phosphofructokinase, platelet type