SMTL ID : 5byb.1

Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP and 1,5-(PA)2-IP4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 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, S.228, P.229, D.273, L.275, C.284, D.285 Ligands: MG.3, MG.4 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:K.151, A:E.201, A:E.201, A:M.204, A:D.210, A:D.273, A:D.285, A:D.285 Water bridges: A:R.98, A:S.228, A:S.228, A:D.273 Salt bridges: A:R.98, A:R.98, A:K.151, A:H.158

1 x 4WY: {[(1R,3S,4S,5R,6S)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl]bis[oxy(2-oxoethane-2,1-diyl)]}bis(phosphonic acid)(Non-covalent)

4WY.2: 10 residues within 4Å: Chain A: K.17, K.18, R.177, K.178, K.212, Y.214, R.226, R.237, S.290, K.293 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:K.212, A:Y.214, A:R.226, A:R.237, A:S.290, A:K.293 Water bridges: A:R.177, A:N.287, A:N.287 Salt bridges: 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.293, A:K.293, A:K.293

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.285, N.287 Ligands: ADP.1, MG.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.285, A:D.285, H2O.4 MG.4: 5 residues within 4Å: Chain A: K.212, D.273, D.285 Ligands: ADP.1, MG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.273, A:D.285, H2O.1, H2O.6 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.7, H2O.8

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 4 residues within 4Å: Chain A: V.85, D.88, L.89, N.90 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.90 Hydrogen bonds: A:L.89 ACT.7: 1 residues within 4Å: Chain A: F.34 No protein-ligand interaction detected (PLIP) ACT.8: 3 residues within 4Å: Chain A: S.181, R.182, K.234 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.181 Salt bridges: A:R.182, A:K.234

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 7 residues within 4Å: Chain A: N.251, R.253, R.276, A.277, G.279, Q.280, S.281 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.253, A:R.253 Water bridges: A:R.253, A:R.276, A:G.279, A:G.279, A:S.281 EDO.10: 5 residues within 4Å: Chain A: Y.220, H.222, K.297, Y.298, D.301 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.301 Water bridges: A:A.223 EDO.11: 3 residues within 4Å: Chain A: N.54, W.55, P.56 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.54 Water bridges: A:L.57 EDO.12: 4 residues within 4Å: Chain A: F.69, P.70, L.71, D.72 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.71, A:D.72 Water bridges: A:H.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Riley, A.M. et al., Synthetic tools for studying the chemical biology of InsP8. Chem.Commun.(Camb.) (2015)

Release Date

2015-07-22

Peptides

Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2

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