SMTL ID : 3t7a.1

Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP at pH 5.2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 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.2, MG.3 23 PLIP interactions: 23 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:A.155, A:H.158, A:K.212, A:K.212, A:K.212, A:K.212, A:K.212, A:S.228, A:S.228, A:D.285, A:D.285, A:N.287 Salt bridges: A:R.98, A:R.98, A:K.151, A:H.158

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.285, N.287 Ligands: ADP.1, MG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.285, A:D.285, H2O.1, H2O.5 MG.3: 4 residues within 4Å: Chain A: D.273, D.285 Ligands: ADP.1, MG.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.273, A:D.285, H2O.1, H2O.5 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.6, H2O.8, H2O.13

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

ACT.5: 5 residues within 4Å: Chain A: A.78, 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: 3 residues within 4Å: Chain A: S.181, R.182, K.234 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.181, A:S.181 Salt bridges: A:R.182, A:K.234 ACT.11: 2 residues within 4Å: Chain A: L.33, F.34 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.33, A:K.35

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

EDO.6: 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.8: 7 residues within 4Å: Chain A: K.212, Y.214, G.271, F.272, D.273, N.287, S.290 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.273, A:N.287, A:S.290, A:S.290 Water bridges: A:D.285 EDO.9: 6 residues within 4Å: Chain A: R.253, R.276, A.277, G.279, Q.280, S.281 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.253, A:G.279, A:G.279 EDO.10: 4 residues within 4Å: Chain A: Y.220, H.222, K.297, Y.298 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.222, A:A.223 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

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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