SMTL ID : 4xyj.2 (1 other biounit)

Crystal structure of human phosphofructokinase-1 in complex with ATP and Mg, Northeast Structural Genomics Consortium Target HR9275

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-tetramer

Ligands

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

ATP.1: 22 residues within 4Å: Chain A: S.60, G.61, G.62, Y.92, R.125, C.126, F.129, R.130, R.135, G.155, D.156, G.157, S.158, T.160, G.161, S.201, D.203, D.205, R.247, R.338 Ligands: MG.2, MG.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.62, A:R.125, A:C.126, A:C.126, A:G.155, A:G.157, A:S.158, A:S.201, A:D.203, A:D.203, A:R.338 Salt bridges: A:R.247, A:R.247 pi-Cation interactions: A:R.130 ATP.5: 23 residues within 4Å: Chain B: S.60, G.61, G.62, Y.92, R.125, C.126, F.129, R.130, R.135, G.154, G.155, D.156, G.157, S.158, T.160, G.161, S.201, D.203, D.205, R.247, R.338 Ligands: MG.6, MG.7 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:G.62, B:C.126, B:C.126, B:R.135, B:G.155, B:G.157, B:S.158, B:T.160, B:S.201, B:S.201, B:R.338 Salt bridges: B:R.125, B:R.125, B:R.247, B:R.247 pi-Cation interactions: B:R.130 ATP.11: 22 residues within 4Å: Chain C: S.60, G.61, G.62, Y.92, R.125, C.126, F.129, R.130, G.154, G.155, D.156, G.157, S.158, T.160, G.161, S.201, D.203, D.205, R.247, R.338 Ligands: MG.12, MG.13 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:S.60, C:S.60, C:G.62, C:R.125, C:C.126, C:C.126, C:G.155, C:G.157, C:S.158, C:S.201, C:D.203, C:D.203, C:R.338 Salt bridges: C:R.125, C:R.247, C:R.247 pi-Cation interactions: C:R.130 ATP.16: 22 residues within 4Å: Chain D: S.60, G.61, G.62, Y.92, R.125, C.126, F.129, R.130, R.135, G.154, G.155, D.156, G.157, S.158, T.160, G.161, S.201, D.203, R.247, R.338 Ligands: MG.17, MG.18 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:S.60, D:G.62, D:R.125, D:C.126, D:C.126, D:R.130, D:R.130, D:G.155, D:D.156, D:G.157, D:S.158, D:T.160, D:S.201, D:R.338 Salt bridges: D:R.125, D:R.247, D:R.247 pi-Cation interactions: D:R.130

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.156, D.205, R.247 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.156 MG.3: 8 residues within 4Å: Chain A: S.60, G.61, G.62, G.154, G.155, G.200, S.201 Ligands: ATP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:G.62, A:G.200 MG.6: 4 residues within 4Å: Chain B: D.156, D.205, R.247 Ligands: ATP.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.156, B:D.205 MG.7: 9 residues within 4Å: Chain B: S.60, G.61, G.62, M.67, G.154, G.155, G.200, S.201 Ligands: ATP.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.60, B:G.62, B:G.200 MG.12: 4 residues within 4Å: Chain C: D.156, D.205, R.247 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.156 MG.13: 9 residues within 4Å: Chain C: S.60, G.61, G.62, M.67, G.154, G.155, G.200, S.201 Ligands: ATP.11 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:S.60, C:G.62, C:G.200 MG.17: 3 residues within 4Å: Chain D: D.156, R.247 Ligands: ATP.16 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.156 MG.18: 8 residues within 4Å: Chain D: S.60, G.62, M.67, G.154, G.155, G.200, S.201 Ligands: ATP.16 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:G.200

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

PO4.4: 6 residues within 4Å: Chain A: G.261, K.292, R.458, R.462, G.495, G.496 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.261, A:G.496 Water bridges: A:R.462 Salt bridges: A:K.292, A:R.458, A:R.462 PO4.8: 4 residues within 4Å: Chain B: R.72, R.76, S.111, S.112 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.112 Salt bridges: B:R.72, B:R.76 PO4.9: 6 residues within 4Å: Chain B: G.261, K.292, R.458, R.462, G.495, G.496 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.261, B:G.496 Salt bridges: B:K.292, B:R.458, B:R.462 PO4.14: 6 residues within 4Å: Chain C: G.261, K.292, R.458, R.462, G.495, G.496 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.261, C:G.496 Salt bridges: C:K.292, C:R.458, C:R.462 PO4.15: 5 residues within 4Å: Chain C: R.72, R.76, S.111, S.112, G.627 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.112, C:G.627 Salt bridges: C:R.72, C:R.76, C:K.595 PO4.19: 6 residues within 4Å: Chain D: G.261, K.292, R.458, R.462, G.495, G.496 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.261, D:G.496, D:T.498 Salt bridges: D:K.292, D:R.458, D:R.462

1 x CO: COBALT (II) ION(Non-covalent)

CO.10: 3 residues within 4Å: Chain B: E.517, K.552, H.553 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.517, B:H.553

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Webb, B.A. et al., Structures of human phosphofructokinase-1 and atomic basis of cancer-associated mutations. Nature (2015)

Release Date

2015-05-20

Peptides

ATP-dependent 6-phosphofructokinase, platelet type: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

ATP-dependent 6-phosphofructokinase, platelet type

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