SMTL ID : 5dgh.1

Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMP-PNP and 5-(PCP)-IP5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 23 residues within 4Å: Chain A: R.98, P.113, V.149, K.151, H.158, V.160, L.175, R.177, E.201, E.202, F.203, M.204, D.210, K.212, S.228, P.229, D.273, L.275, C.284, D.285, N.287 Ligands: MG.3, MG.4 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:R.98, A:R.98, A:K.151, A:H.158, A:R.177, A:R.177, A:E.201, A:E.201, A:M.204, A:D.210, A:K.212, A:D.273, A:D.285, A:N.287 Water bridges: A:S.228, A:S.228, A:N.287 Salt bridges: A:R.98, A:K.151

1 x 5A3: Methylenebisphosphonate inositol pentakisphosphate(Non-covalent)

5A3.2: 12 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 Ligands: MG.7, EDO.10 31 PLIP interactions: 31 interactions with chain A Hydrogen bonds: A:K.178, A:R.237, A:R.237, A:S.290, A:S.290 Water bridges: A:K.17, A:K.17, A:K.17, A:K.18, A:K.18, A:K.18, A:S.21, A:R.177, A:R.177, A:R.177, A:K.178, A:F.289, A:F.289 Salt bridges: A:K.17, A:K.17, A:K.18, A:K.18, A:K.18, A:R.177, A:K.178, A:K.212, A:R.226, A:R.226, A:K.293, A:K.293, A:K.293

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

MG.3: 4 residues within 4Å: Chain A: D.285, N.287 Ligands: ANP.1, MG.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.285, A:D.285, H2O.3 MG.4: 4 residues within 4Å: Chain A: D.273, D.285 Ligands: ANP.1, MG.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.273, A:D.285, H2O.3 MG.5: 3 residues within 4Å: Chain A: S.32, F.34, I.37 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:F.34, A:I.37, H2O.2, H2O.6, H2O.8 MG.6: 1 residues within 4Å: Chain A: N.287 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Ligands: 5A3.2 No protein-ligand interaction detected (PLIP)

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

EDO.8: 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.10: 9 residues within 4Å: Chain A: K.212, V.213, Y.214, G.271, F.272, D.273, N.287, S.290 Ligands: 5A3.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.272, A:N.287, A:S.290, A:S.290 EDO.11: 5 residues within 4Å: Chain A: R.276, A.277, G.279, Q.280, S.281 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.251, A:A.277, A:Q.280 EDO.12: 5 residues within 4Å: Chain A: Y.220, H.222, K.297, Y.298, D.301 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.301 Water bridges: A:Y.220, A:A.221, A:A.223 EDO.14: 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 EDO.15: 4 residues within 4Å: Chain A: V.85, D.88, L.89, N.90 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.89, A:N.90, A:N.90 Water bridges: A:D.88, A:D.88

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

ACT.9: 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 ACT.13: 1 residues within 4Å: Chain A: F.34 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hager, A. et al., Cellular Cations Control Conformational Switching of Inositol Pyrophosphate Analogues. Chemistry (2016)

Release Date

2016-08-10

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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