SMTL ID : 3t9e.1

Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP, 5-(PP)-IP5 (5-IP7) and MgF3 (transition state mimic)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

ADP.1: 20 residues within 4Å: Chain A: R.98, P.113, V.149, K.151, H.158, V.160, L.175, E.201, E.202, F.203, M.204, D.210, P.229, D.273, L.275, C.284, D.285 Ligands: MG.3, MG.4, MGF.8 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:K.151, A:E.201, A:E.201, A:M.204, A:D.210, A:D.285 Water bridges: A:R.98, A:T.206, A:K.212, A:R.226 Salt bridges: A:R.98, A:R.98, A:K.151, A:H.158

1 x I7P: (1r,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate(Non-covalent)

I7P.2: 14 residues within 4Å: Chain A: K.17, K.18, R.177, K.178, K.212, R.226, R.237, E.243, R.245, N.287, S.290, K.293 Ligands: MG.6, MGF.8 45 PLIP interactions: 45 interactions with chain A Hydrogen bonds: A:K.178, A:N.287 Water bridges: A:K.17, A:K.17, A:K.18, A:K.18, A:K.18, A:E.156, A:R.177, A:K.178, A:K.212, A:R.226, A:R.226, A:R.226, A:E.243, A:R.245, A:R.245, A:R.245, A:N.287, A:N.287, A:N.287, A:S.290, A:S.290, A:S.290, A:S.290, A:K.293, A:K.293 Salt bridges: A:K.17, A:K.17, A:K.18, A:K.18, A:K.18, A:R.177, A:R.177, A:K.178, A:K.178, A:K.178, A:K.212, A:K.212, A:R.226, A:R.237, A:R.245, A:K.293, A:K.293, A:K.293

5 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 5 residues within 4Å: Chain A: D.285, N.287 Ligands: ADP.1, MG.4, MGF.8 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.285, A:D.285, H2O.17 MG.4: 6 residues within 4Å: Chain A: K.212, D.273, D.285 Ligands: ADP.1, MG.3, MGF.8 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.273, A:D.285, H2O.1 MG.5: 3 residues within 4Å: Chain A: S.32, F.34, I.37 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.32, A:F.34, A:I.37, H2O.4, H2O.12 MG.6: 1 residues within 4Å: Ligands: I7P.2 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain A: N.287 No protein-ligand interaction detected (PLIP)

1 x MGF: TRIFLUOROMAGNESATE(Non-covalent)

MGF.8: 10 residues within 4Å: Chain A: H.158, R.177, K.212, D.273, D.285, N.287 Ligands: ADP.1, I7P.2, MG.3, MG.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., Structural basis for an inositol pyrophosphate kinase surmounting phosphate crowding. Nat.Chem.Biol. (2011)

Release Date

2011-12-07

Peptides

Inositol Pyrophosphate Kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Inositol Pyrophosphate Kinase

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