SMTL ID : 3udt.3 (2 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-dimer

Ligands

2 x 5MY: MYO-INOSITOL-(1,3,4,5,6)-PENTAKISPHOSPHATE(Non-covalent)

5MY.1: 14 residues within 4Å: Chain A: G.54, A.55, R.79, R.164, K.202, K.204, H.230, K.234, N.272, D.402, K.445, R.449, Y.453, L.456 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:G.54, A:K.202, A:K.202, A:H.230, A:N.272, A:Y.453 Salt bridges: A:R.79, A:R.164, A:K.202, A:K.202, A:K.204, A:K.204, A:H.230, A:K.234, A:K.234, A:K.445, A:K.445, A:R.449, A:R.449 5MY.5: 14 residues within 4Å: Chain B: G.54, A.55, R.79, R.164, K.202, K.204, H.230, K.234, N.272, D.402, K.445, R.449, Y.453, L.456 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:G.54, B:K.202, B:K.202, B:N.272, B:D.402 Salt bridges: B:R.79, B:R.164, 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: 19 residues within 4Å: Chain A: R.50, 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, D.441 Ligands: MG.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.50, A:G.53, A:G.54, A:A.55, A:N.56, A:N.181, A:D.182, A:H.183, A:E.200 Salt bridges: A:R.74, A:R.74 ADP.6: 21 residues within 4Å: Chain B: R.50, 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: MG.7 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:R.50, B:G.53, B:G.54, B:A.55, B:N.56, B:N.181, B:H.183, B:E.200, B:S.443, B:S.443 Salt bridges: B:R.74, B:R.74

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.402, S.404, D.441 Ligands: ADP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.441 MG.7: 4 residues within 4Å: Chain B: E.200, S.404, D.441 Ligands: ADP.6 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: H.354, C.364, C.367, H.380 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.354, A:C.364, A:C.367, A:H.380 ZN.8: 4 residues within 4Å: Chain B: H.354, C.364, C.367, H.380 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.354, B:C.364, B:C.367, B:H.380

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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