SMTL ID : 8e1h.1 (1 other biounit)

Asp1 kinase in complex with ADP Mg 5-IP7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

ADP.1: 20 residues within 4Å: Chain A: R.94, P.109, V.166, K.168, H.175, I.177, L.192, E.219, E.220, F.221, M.222, D.229, S.247, P.248, D.292, L.294, I.303, D.304 Ligands: MG.3, MG.4 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:K.168, A:E.219, A:E.219, A:M.222, A:D.229, A:D.292, A:D.292 Water bridges: A:K.231, A:S.247, A:D.292, A:N.306 Salt bridges: A:R.94, A:R.94, A:K.168, A:H.175

1 x I7P: (1r,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate(Non-covalent)

I7P.2: 9 residues within 4Å: Chain A: K.14, R.194, K.195, R.245, R.256, K.261, R.264, K.312 Ligands: MG.5 19 PLIP interactions: 19 interactions with chain A Water bridges: A:E.173, A:K.195, A:K.195, A:K.195, A:K.195 Salt bridges: A:K.14, A:K.14, A:K.14, A:R.194, A:R.194, A:K.195, A:K.195, A:K.195, A:R.245, A:R.256, A:R.264, A:K.312, A:K.312, A:K.312

3 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 4 residues within 4Å: Chain A: D.292, D.304 Ligands: ADP.1, MG.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.292, A:D.304, H2O.2, H2O.5 MG.4: 4 residues within 4Å: Chain A: D.304, N.306 Ligands: ADP.1, MG.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.304, H2O.2, H2O.7 MG.5: 1 residues within 4Å: Ligands: I7P.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Benjamin, B. et al., Structures of Fission Yeast Inositol Pyrophosphate Kinase Asp1 in Ligand-Free, Substrate-Bound, and Product-Bound States. Mbio (2022)

Release Date

2022-11-30

Peptides

Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase

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