SMTL ID : 3t9a.1

Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMPPNP at pH 7.0

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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.2, MG.3 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:E.201, A:E.201, A:M.204, A:D.210, A:K.212, A:D.285, A:N.287 Water bridges: A:Y.102, A:H.158, A:T.206, A:S.228, A:N.287 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.10 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.2 MG.4: 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.2, H2O.9 MG.7: 6 residues within 4Å: Chain A: T.215, C.262, Q.267, T.268, V.269, C.270 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:T.215, A:C.262, A:Q.267, A:T.268

2 x CD: CADMIUM ION(Non-covalent)

CD.5: 1 residues within 4Å: Chain A: C.128 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:C.128, H2O.1, H2O.8, H2O.11, H2O.15 CD.6: 1 residues within 4Å: Chain A: C.128 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:C.128, H2O.11, H2O.13, H2O.15

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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