SMTL ID : 4u1r.1

ATP-bound structure of human platelet phosphofructokinase in an R-state, crystal form II

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

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

ATP.1: 16 residues within 4Å: Chain A: S.13, G.14, G.15, Y.45, A.77, R.78, C.79, F.82, R.83, G.108, D.109, G.110, S.111, G.114, L.117, D.158 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.13, A:G.15, A:C.79, A:C.79, A:R.83, A:R.83, A:G.108, A:G.108, A:D.109, A:D.109, A:G.110, A:S.111, A:D.158, A:D.158 pi-Cation interactions: A:R.83 ATP.6: 17 residues within 4Å: Chain B: S.13, G.14, G.15, Y.45, A.77, R.78, C.79, F.82, R.83, G.108, D.109, G.110, S.111, G.114, L.117, D.156, D.158 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.13, B:G.15, B:C.79, B:C.79, B:G.108, B:D.109, B:D.109, B:G.110, B:S.111, B:D.156, B:D.158 pi-Cation interactions: B:R.83 ATP.9: 14 residues within 4Å: Chain C: S.13, G.14, G.15, Y.45, R.78, C.79, F.82, R.83, G.108, D.109, G.110, S.111, G.114, L.117 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:S.13, C:G.15, C:C.79, C:C.79, C:R.83, C:G.108, C:D.109, C:D.109, C:G.110, C:S.111 pi-Cation interactions: C:R.83 ATP.14: 17 residues within 4Å: Chain D: S.13, G.14, G.15, Y.45, A.77, R.78, C.79, F.82, R.83, G.108, D.109, G.110, S.111, G.114, L.117, D.156, D.158 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:S.13, D:G.15, D:C.79, D:C.79, D:G.108, D:G.108, D:D.109, D:D.109, D:G.110, D:S.111, D:D.156, D:D.158 pi-Cation interactions: D:R.83

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

PO4.2: 6 residues within 4Å: Chain A: G.214, K.245, R.411, R.415, G.448, G.449 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.449 Salt bridges: A:K.245, A:R.411, A:R.415 PO4.3: 5 residues within 4Å: Chain A: R.557, R.646 Chain B: A.401, R.462, H.652 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.462, B:H.652, A:R.557, A:R.646 PO4.4: 8 residues within 4Å: Chain A: R.25, R.29, V.63, S.64, S.65, K.548, G.580, R.613 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.65 Salt bridges: A:R.25, A:R.29, A:K.548, A:R.613 PO4.5: 4 residues within 4Å: Chain A: R.462, H.652 Chain B: R.557, R.646 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.462, A:H.652, B:R.557, B:R.646 PO4.7: 6 residues within 4Å: Chain B: G.214, K.245, R.411, R.415, G.448, G.449 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.449 Salt bridges: B:K.245, B:R.411, B:R.415 PO4.8: 7 residues within 4Å: Chain B: R.25, R.29, S.64, S.65, K.548, G.580, R.613 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.65, B:G.580 Salt bridges: B:R.25, B:R.29, B:K.548, B:R.613 PO4.10: 6 residues within 4Å: Chain C: G.214, K.245, R.411, R.415, G.448, G.449 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.449 Salt bridges: C:K.245, C:R.411, C:R.415 PO4.11: 5 residues within 4Å: Chain C: R.557, R.646 Chain D: A.401, R.462, H.652 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Salt bridges: D:R.462, D:H.652, C:R.557, C:R.646 PO4.12: 7 residues within 4Å: Chain C: R.25, R.29, V.63, S.64, S.65, G.580, R.613 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.65 Salt bridges: C:R.25, C:R.29, C:K.548, C:R.613 PO4.13: 4 residues within 4Å: Chain C: R.462, H.652 Chain D: R.557, R.646 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Salt bridges: C:R.462, C:H.652, D:R.557, D:R.646 PO4.15: 7 residues within 4Å: Chain D: G.214, D.216, K.245, R.411, R.415, G.448, G.449 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.216, D:G.449 Salt bridges: D:K.245, D:R.411, D:R.415 PO4.16: 8 residues within 4Å: Chain D: R.25, R.29, V.63, S.64, S.65, K.548, G.580, R.613 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.65 Salt bridges: D:R.25, D:R.29, D:K.548, D:R.613

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kloos, M. et al., Crystal structure of human platelet phosphofructokinase-1 locked in an activated conformation. Biochem.J. (2015)

Release Date

2015-06-03

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

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