SMTL ID : 3t54.1

Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ATP and Cadmium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 24 residues within 4Å: Chain A: R.102, P.117, V.153, K.155, H.162, V.164, L.179, R.181, E.205, E.206, F.207, M.208, D.214, K.216, S.232, P.233, D.277, L.279, C.288, D.289, N.291 Ligands: CD.2, CD.3, CD.7 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:E.206, A:M.208, A:D.214, A:D.277, A:D.277 Water bridges: A:K.155, A:R.181, A:R.181, A:R.181, A:R.181, A:D.214, A:K.216, A:K.216, A:S.232 Salt bridges: A:R.102, A:R.102, A:K.155, A:H.162, A:H.162, A:R.181, A:K.216

6 x CD: CADMIUM ION(Non-covalent)

CD.2: 3 residues within 4Å: Chain A: D.289, N.291 Ligands: ATP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.289, A:D.289, H2O.4 CD.3: 4 residues within 4Å: Chain A: K.216, D.277, D.289 Ligands: ATP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.277, A:D.289, H2O.4 CD.4: 6 residues within 4Å: Chain A: T.219, C.266, Q.271, T.272, V.273, C.274 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.219, A:C.266, A:Q.271, A:T.272, A:C.274 CD.5: 1 residues within 4Å: Chain A: C.132 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:C.132, H2O.4, H2O.4, H2O.11 CD.6: 1 residues within 4Å: Chain A: C.132 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:C.132, H2O.11, H2O.11, H2O.12 CD.7: 5 residues within 4Å: Chain A: Y.106, K.155, E.205, C.288 Ligands: ATP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.205, A:C.288

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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