SMTL ID : 9fw6.2 (1 other biounit)

A ternary complex of plant adenosine kinase 1 from moss Physcomitrella patens (PpADK1) with adenosine and ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

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

ADP.1: 20 residues within 4Å: Chain A: R.147, N.237, T.279, Q.280, G.281, T.282, T.285, V.298, T.299, P.300, I.301, L.306, T.309, A.312, G.313, F.316, N.338, A.341, S.342, I.345 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:N.237, A:T.279, A:T.279, A:G.281, A:T.285, A:I.301, A:G.313, A:N.338 Water bridges: A:R.147, A:R.147, A:E.238, A:E.240, A:Q.280, A:A.311, A:S.342 Salt bridges: A:R.147

1 x ADN: ADENOSINE(Non-covalent)

ADN.2: 22 residues within 4Å: Chain A: N.30, L.32, D.34, A.54, L.56, G.79, G.80, A.81, T.82, N.84, C.138, V.140, R.147, L.149, A.151, L.153, F.184, F.215, N.310, A.311, D.314 Ligands: NA.5 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.30, A:G.80, A:A.81, A:N.84, A:N.310, A:A.311, A:D.314 Water bridges: A:R.147 pi-Stacking: A:F.184, A:F.184

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

EDO.3: 3 residues within 4Å: Chain A: Q.218, F.219, K.221 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.221 EDO.4: 4 residues within 4Å: Chain A: L.56, F.215, F.219, F.220 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 7 residues within 4Å: Chain A: G.29, N.30, A.81, T.82, A.182, F.184 Ligands: ADN.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.30, A:A.81, A:T.82, A:T.82, A:T.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kopecny, D.J. et al., A monomer-dimer switch modulates the activity of plant adenosine kinase. J.Exp.Bot. (2025)

Release Date

2025-04-09

Peptides

Adenosine kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Adenosine kinase

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