SMTL ID : 8rpa.1

Crystal structure of Zea mays adenosine kinase 3 (ZmADK3) in complex with AP5A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

monomer

Ligands

1 x AP5: BIS(ADENOSINE)-5'-PENTAPHOSPHATE(Non-covalent)

AP5.1: 40 residues within 4Å: Chain A: N.32, L.34, D.36, L.58, G.81, G.82, A.83, N.86, C.140, V.142, R.149, L.151, A.153, L.155, F.186, T.189, F.217, N.239, T.281, Q.282, G.283, C.284, V.287, V.300, I.301, L.302, L.303, L.308, T.311, N.312, G.313, A.314, G.315, D.316, F.318, C.340, A.343, N.344, I.347 Ligands: CL.7 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:N.32, A:D.36, A:D.36, A:G.82, A:A.83, A:N.86, A:N.239, A:T.281, A:G.283, A:N.312, A:G.313, A:G.313, A:A.314, A:G.315, A:D.316, A:C.340 Water bridges: A:D.36, A:R.149, A:I.301 Salt bridges: A:R.149, A:R.149 pi-Stacking: A:F.186, A:F.186

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

EDO.2: 3 residues within 4Å: Chain A: K.167, W.172, L.197 No protein-ligand interaction detected (PLIP)

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 3 residues within 4Å: Chain A: A.204, T.205, N.206 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.204, A:N.206 PEG.4: 5 residues within 4Å: Chain A: P.231, Y.232, P.268, K.269, A.270 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.232 PEG.5: 5 residues within 4Å: Chain A: L.35, Y.78, K.111, F.112, E.115 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.111

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain A: K.73, S.74, N.75 Ligand excluded by PLIP CL.7: 8 residues within 4Å: Chain A: G.31, N.32, A.83, T.84, A.184, F.186, F.187 Ligands: AP5.1 Ligand excluded by PLIP

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

2025-01-29

Peptides

Adenosine kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Adenosine kinase