SMTL ID : 6gfh.2 (1 other biounit)

Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with neo-IP5 and ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

1 x K7V: neo-Inositol pentakisphosphate(Non-covalent)

K7V.1: 14 residues within 4Å: Chain A: G.39, A.40, R.149, K.187, K.189, K.219, N.257, D.387, K.430, R.434, Y.438 Ligands: ATP.2, MG.4, EDO.7 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:G.39, A:K.187, A:N.257, A:D.387, A:Y.438 Water bridges: A:K.189, A:K.189, A:K.189 Salt bridges: A:R.149, A:K.187, A:K.187, A:K.189, A:K.219, A:K.430, A:K.430, A:R.434, A:R.434

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

ATP.2: 26 residues within 4Å: Chain A: R.35, G.36, E.37, G.38, G.39, A.40, N.41, V.43, V.57, R.59, L.165, N.166, D.167, H.168, S.169, E.185, K.187, R.260, F.262, D.387, M.391, I.425, D.426 Ligands: K7V.1, MG.3, MG.4 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.39, A:A.40, A:N.41, A:N.41, A:N.166, A:H.168, A:H.168, A:E.185, A:E.185, A:R.260, A:D.426 Salt bridges: A:R.59, A:R.59, A:K.187

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.387, S.389, D.426 Ligands: ATP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.387, A:S.389 MG.4: 5 residues within 4Å: Chain A: D.387, D.426, S.428 Ligands: K7V.1, ATP.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.426, A:D.426, A:S.428

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: H.339, C.349, C.352, H.365 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.339, A:C.349, A:C.352, A:H.365

1 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.6: 9 residues within 4Å: Chain A: D.343, P.348, C.349, H.365, A.366, L.367, P.368, L.369, S.372 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:H.365 Hydrogen bonds: A:C.349, A:L.367, A:L.367, A:S.372 Water bridges: A:D.343, A:H.365

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

EDO.7: 5 residues within 4Å: Chain A: G.39, R.64, W.148, R.149 Ligands: K7V.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.149

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Whitfield, H. et al., A Fluorescent Probe Identifies Active Site Ligands of Inositol Pentakisphosphate 2-Kinase. J. Med. Chem. (2018)

Release Date

2018-09-12

Peptides

Inositol-pentakisphosphate 2-kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Inositol-pentakisphosphate 2-kinase

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