SMTL ID : 5dgi.1

Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP and 3,5-(PCP)2-IP4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 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 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:K.151, A:E.201, A:E.201, A:M.204, A:D.210, A:D.285, A:D.285 Water bridges: A:R.98, A:K.212, A:S.228, A:S.228 Salt bridges: A:R.98, A:R.98, A:K.151, A:H.158

1 x 5A2: 3,5-di-methylenebisphosphonate inositol tetrakisphosphate(Non-covalent)

5A2.2: 11 residues within 4Å: Chain A: K.17, K.18, S.66, K.67, R.177, K.178, Y.214, R.226, S.290, K.293 Ligands: EDO.9 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:K.17, A:K.17, A:K.18, A:K.18, A:K.67, A:R.177, A:R.177, A:K.178, A:S.290 Water bridges: A:E.156, A:E.156, A:Y.214, A:Y.214, A:N.287, A:N.287 Salt bridges: A:K.17, A:K.18, A:K.18, A:R.177, A:K.178, A:R.226, A:R.226, 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 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.285, A:D.285, H2O.1, H2O.8 MG.4: 4 residues within 4Å: Chain A: 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.2, H2O.10 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.6

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

ACT.6: 4 residues within 4Å: Chain A: V.85, D.88, L.89, N.90 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.90 Hydrogen bonds: A:D.88, A:L.89 ACT.8: 3 residues within 4Å: Chain A: S.181, R.182, K.234 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.182, A:K.234 ACT.12: 1 residues within 4Å: Chain A: F.34 No protein-ligand interaction detected (PLIP)

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

EDO.7: 3 residues within 4Å: Chain A: N.54, W.55, P.56 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.54 EDO.9: 9 residues within 4Å: Chain A: K.212, V.213, Y.214, G.271, F.272, D.273, N.287, S.290 Ligands: 5A2.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.273, A:N.287, A:S.290, A:S.290 Water bridges: A:Y.214, A:D.285 EDO.10: 6 residues within 4Å: Chain A: R.253, R.276, A.277, G.279, Q.280, S.281 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.253, A:G.279, A:G.279, A:G.279 EDO.11: 4 residues within 4Å: Chain A: Y.220, H.222, K.297, Y.298 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.301 Water bridges: A:Y.220, A:H.222, A:A.223 EDO.13: 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

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

Related Entries With Identical Sequence