SMTL ID : 6fl8.1 (1 other biounit)

Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with purpurogallin and ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x TIY: 2,3,4,6-tetrahydroxy-5H-benzo[7]annulen-5-one(Non-covalent)

TIY.1: 12 residues within 4Å: Chain A: G.38, G.39, R.149, K.187, K.189, H.215, K.219, N.257, D.387 Ligands: ADP.2, MG.3, EDO.5 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.39, A:R.149, A:R.149, A:K.187, A:K.189, A:K.189, A:K.219, A:N.257 Water bridges: A:K.187, A:H.215, A:H.215 pi-Cation interactions: A:K.187

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 23 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, R.260, F.262, M.391, I.425, D.426 Ligands: TIY.1, MG.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:R.35, A:G.38, A:G.39, A:A.40, A:N.41, A:N.41, A:N.166, A:H.168, A:E.185, A:E.185 Water bridges: A:E.37, A:R.260 Salt bridges: A:R.59, A:R.59

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.426 Ligands: TIY.1, ADP.2 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.426, H2O.4, H2O.4

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 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

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

EDO.5: 7 residues within 4Å: Chain A: K.219, E.224, I.225, Q.256, N.257, S.275 Ligands: TIY.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.257 Water bridges: A:Q.216, A:N.257 EDO.6: 6 residues within 4Å: Chain A: C.190, F.192, P.194, D.330, D.333, K.386 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.192, A:D.330, A:D.333 Water bridges: A:I.334, A:K.386

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
A

Inositol-pentakisphosphate 2-kinase

Related Entries With Identical Sequence