SMTL ID : 3udz.1 (2 other biounits)

Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with ADP and IP6.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 18 residues within 4Å: Chain A: G.53, G.54, A.55, R.79, R.164, K.202, K.204, H.230, K.234, N.272, D.402, D.441, K.445, R.449, Y.453 Ligands: ADP.2, MG.3, MG.4 28 PLIP interactions: 26 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.54, A:A.55, A:R.79, A:N.272, A:D.402 Water bridges: A:R.164, A:K.204, A:K.234, A:K.234, A:K.234, A:K.445, A:K.445, A:R.449, A:R.449, A:R.449, B:R.212, B:R.212 Salt bridges: A:R.164, A:K.202, A:K.202, A:K.202, A:K.204, A:K.204, A:K.234, A:K.445, A:K.445, A:R.449, A:R.449 IHP.5: 18 residues within 4Å: Chain B: G.53, G.54, A.55, R.79, R.164, K.202, K.204, H.230, K.234, N.272, D.402, D.441, K.445, R.449, Y.453 Ligands: ADP.6, MG.7, MG.8 28 PLIP interactions: 28 interactions with chain B Hydrogen bonds: B:G.54, B:N.272, B:D.402, B:D.402, B:Y.453 Water bridges: B:R.164, B:R.164, B:K.202, B:K.204, B:K.204, B:K.204, B:R.226, B:K.234, B:S.443, B:K.445 Salt bridges: B:R.79, B:R.164, B:K.202, B:K.202, B:K.202, B:K.204, B:K.204, B:H.230, B:K.234, B:K.445, B:K.445, B:R.449, B:R.449

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

ADP.2: 22 residues within 4Å: Chain A: E.52, G.53, G.54, A.55, N.56, V.58, V.72, R.74, L.180, N.181, D.182, H.183, E.200, R.275, F.277, M.406, I.440, D.441, S.443 Ligands: IHP.1, MG.3, MG.4 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.53, A:G.54, A:A.55, A:N.56, A:N.56, A:N.181, A:H.183, A:E.200, A:D.441, A:S.443 Water bridges: A:E.200, A:D.441 Salt bridges: A:R.74, A:R.74 ADP.6: 21 residues within 4Å: Chain B: E.52, G.53, G.54, A.55, N.56, V.58, V.72, R.74, L.180, N.181, D.182, H.183, E.200, R.275, M.406, I.440, D.441, S.443 Ligands: IHP.5, MG.7, MG.8 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:G.53, B:A.55, B:N.56, B:N.56, B:N.181, B:D.182, B:H.183, B:E.200, B:R.275, B:S.443 Water bridges: B:R.50, B:R.74, B:D.441 Salt bridges: B:R.74, B:R.74

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.441, S.443 Ligands: IHP.1, ADP.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.441, H2O.1 MG.4: 3 residues within 4Å: Chain A: D.441 Ligands: IHP.1, ADP.2 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.441, H2O.2, H2O.5 MG.7: 4 residues within 4Å: Chain B: D.441, S.443 Ligands: IHP.5, ADP.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.441, B:S.443, H2O.11 MG.8: 3 residues within 4Å: Chain B: D.441 Ligands: IHP.5, ADP.6 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.9: 3 residues within 4Å: Chain B: H.354, C.364, H.380 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.354, B:C.364, B:H.380, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gosein, V. et al., Inositol phosphate-induced stabilization of inositol 1,3,4,5,6-pentakisphosphate 2-kinase and its role in substrate specificity. Protein Sci. (2012)

Release Date

2012-03-14

Peptides

Inositol pentakisphosphate 2-kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Inositol pentakisphosphate 2-kinase

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