SMTL ID : 4xyk.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

homo-tetramer

Ligands

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 12 residues within 4Å: Chain A: S.60, G.61, G.62, Y.92, R.125, C.126, R.130, G.155, D.156, G.157, S.158, G.161 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.60, A:G.62, A:C.126, A:C.126, A:R.130, A:G.155, A:D.156, A:D.156, A:G.157, A:S.158, A:S.158 Salt bridges: A:R.125 pi-Cation interactions: A:R.130 ADP.5: 14 residues within 4Å: Chain B: G.61, G.62, Y.92, R.125, C.126, R.130, G.154, G.155, D.156, G.157, S.158, G.161, S.201, R.247 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.62, B:R.125, B:C.126, B:C.126, B:R.130, B:G.155, B:D.156, B:G.157, B:S.158, B:S.201, B:R.247 pi-Cation interactions: B:R.130 ADP.8: 15 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, G.161, L.164 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.62, C:R.125, C:C.126, C:C.126, C:R.130, C:R.130, C:G.155, C:D.156, C:G.157, C:S.158 pi-Cation interactions: C:R.130 ADP.14: 14 residues within 4Å: Chain D: S.60, G.61, Y.92, R.125, C.126, F.129, R.130, G.154, G.155, D.156, G.157, S.158, G.161, L.164 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:R.125, D:C.126, D:C.126, D:R.130, D:G.155, D:D.156, D:G.157, D:S.158 pi-Cation interactions: D:R.130

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

PO4.2: 6 residues within 4Å: Chain A: G.261, K.292, R.458, R.462, G.495, G.496 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.496 Salt bridges: A:K.292, A:R.458, A:R.462 PO4.3: 7 residues within 4Å: Chain A: R.72, R.76, V.110, S.111, S.112, R.660, L.789 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.111, A:S.111, A:S.112, A:G.627, A:R.660 Salt bridges: A:R.72, A:R.76 PO4.4: 5 residues within 4Å: Chain A: A.448, R.509, H.699 Chain B: R.604, R.693 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.509, A:H.699, B:R.604, B:R.693 PO4.6: 6 residues within 4Å: Chain B: G.261, K.292, R.458, R.462, G.495, G.496 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.496 Salt bridges: B:K.292, B:R.458, B:R.462 PO4.7: 7 residues within 4Å: Chain B: R.72, R.76, V.110, S.111, S.112, G.627, R.660 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.112 Salt bridges: B:R.72, B:R.76, B:R.660 PO4.9: 6 residues within 4Å: Chain C: G.261, K.292, R.458, R.462, G.495, G.496 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.496 Salt bridges: C:K.292, C:R.458, C:R.462 PO4.10: 7 residues within 4Å: Chain C: R.72, R.76, V.110, S.111, S.112, G.627, R.660 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.112 Salt bridges: C:R.72, C:R.76, C:R.660 PO4.11: 5 residues within 4Å: Chain C: R.509, H.699, Q.702 Chain D: R.604, R.693 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.509 Salt bridges: C:H.699, D:R.604, D:R.693 PO4.12: 6 residues within 4Å: Chain C: R.125, R.247, H.335, R.338 Chain D: R.238, R.329 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Salt bridges: C:R.125, C:R.247, C:H.335, C:R.338, D:R.238, D:R.329 PO4.13: 4 residues within 4Å: Chain C: R.604, R.693 Chain D: 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 PO4.15: 6 residues within 4Å: Chain D: G.261, K.292, R.458, R.462, G.495, G.496 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.261, D:G.496 Salt bridges: D:K.292, D:R.458, D:R.462 PO4.16: 9 residues within 4Å: Chain D: R.72, R.76, V.110, S.111, S.112, Q.115, K.595, G.627, R.660 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.111, D:S.112, D:Q.115 Salt bridges: D:R.72, D:R.76, D:K.595, D:R.660

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

2015-05-06

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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