SMTL ID : 3ehg.1

Crystal structure of the ATP-binding domain of DesK in complex with ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

monomer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 18 residues within 4Å: Chain A: E.47, N.51, V.52, K.54, H.55, S.56, D.78, T.81, F.82, K.83, G.84, S.88, G.92, H.93, G.94, L.95, T.117 Ligands: MG.2 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:E.47, A:N.51, A:D.78, A:K.83, A:G.94, A:L.95, A:T.117 Water bridges: A:V.52, A:K.54, A:K.54, A:H.55, A:H.55, A:L.96 Salt bridges: A:K.54, A:K.54, A:H.55, A:H.93, A:H.93 pi-Cation interactions: A:H.55

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.47, N.51 Ligands: ATP.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.47, H2O.6

12 x IOD: IODIDE ION(Non-functional Binders)

IOD.3: 3 residues within 4Å: Chain A: R.99, H.110, I.111 Ligand excluded by PLIP IOD.4: 3 residues within 4Å: Chain A: S.77, D.78, D.79 Ligand excluded by PLIP IOD.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.6: 4 residues within 4Å: Chain A: G.1, R.3, L.35, N.39 Ligand excluded by PLIP IOD.7: 2 residues within 4Å: Chain A: E.85, S.88 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: I.14, V.53 Ligand excluded by PLIP IOD.9: 4 residues within 4Å: Chain A: L.36, R.101, F.104, A.105 Ligand excluded by PLIP IOD.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.12: 1 residues within 4Å: Chain A: E.100 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain A: E.86, S.88, F.89 Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Chain A: D.19, I.20 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Trajtenberg, F. et al., Structural and enzymatic insights into the ATP binding and autophosphorylation mechanism of a sensor histidine kinase. J.Biol.Chem. (2010)

Release Date

2009-09-15

Peptides

Sensor kinase (YocF protein): A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Sensor kinase (YocF protein)