SMTL ID : 6n5c.1

Crystal structure of the catalytic domain of PPIP5K2 in complex with AMPPNP and 5-PCF2Am-InsP5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

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

ANP.1: 24 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.2, MG.3, KDJ.6 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:R.98, A:R.98, A:K.151, A:H.158, A:H.158, A:R.177, A:E.201, A:E.201, A:M.204, A:D.210, A:K.212, A:D.285, A:N.287 Water bridges: A:S.228, A:S.228 Salt bridges: A:R.98, A:K.151

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.285, N.287 Ligands: ANP.1, MG.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.285, A:D.285, H2O.4 MG.3: 4 residues within 4Å: Chain A: D.273, D.285 Ligands: ANP.1, MG.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.273, A:D.285, H2O.3 MG.4: 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.8, H2O.10 MG.5: 2 residues within 4Å: Chain A: N.287 Ligands: KDJ.6 No protein-ligand interaction detected (PLIP)

1 x KDJ: (1,1-difluoro-2-oxo-2-{[(1s,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl]amino}ethyl)phosphonic acid(Non-covalent)

KDJ.6: 13 residues within 4Å: Chain A: K.17, K.18, R.177, K.178, K.212, R.226, R.237, E.243, S.290, K.293 Ligands: ANP.1, MG.5, EDO.10 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:R.177, A:R.177, A:K.178, A:R.237, A:R.237, A:S.290 Water bridges: A:K.17, A:K.17, A:K.18, A:K.18, A:K.18, A:K.18, A:K.212, A:N.287, A:S.290 Salt bridges: 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:K.293, A:K.293, A:K.293

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

ACT.7: 5 residues within 4Å: Chain A: A.78, 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.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)

5 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: KDJ.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.213, A:V.213, A:F.272, A:N.287, A:S.290 EDO.11: 7 residues within 4Å: Chain A: N.251, R.253, R.276, A.277, G.279, Q.280, S.281 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.277 EDO.12: 3 residues within 4Å: Chain A: Y.220, H.222, Y.298 2 PLIP interactions: 2 interactions with chain A Water bridges: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Riley, A.M. et al., Synthesis of an alpha-phosphono-alpha , alpha-difluoroacetamide analogue of the diphosphoinositol pentakisphosphate 5-InsP7. Medchemcomm (2019)

Release Date

2019-08-21

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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