SMTL ID : 4azw.1

Crystal structure of monomeric WbdD.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

monomer

Ligands

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

ATP.1: 21 residues within 4Å: Chain A: P.242, Y.243, H.250, R.254, Y.256, F.258, V.263, K.265, F.267, E.287, M.321, E.322, K.323, L.324, L.328, W.368, N.369, I.381, D.382 Ligands: MG.3, MG.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.256, A:E.322, A:L.324, A:D.382, A:D.382 Water bridges: A:W.368 Salt bridges: A:H.250, A:R.254, A:K.265, A:K.265

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.2: 17 residues within 4Å: Chain A: Y.29, Q.30, R.49, G.74, A.76, F.80, D.95, F.96, Q.97, N.100, G.121, R.122, I.123, E.124, L.141, S.142, V.143 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.29, A:A.76 Hydrogen bonds: A:Q.30, A:G.74, A:A.76, A:F.96, A:Q.97, A:N.100, A:I.123, A:E.124 Water bridges: A:L.141 Salt bridges: A:R.44, A:R.49 pi-Stacking: A:F.96, A:F.96 pi-Cation interactions: A:Y.29

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: N.369, D.382 Ligands: ATP.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.382, H2O.69 MG.4: 4 residues within 4Å: Chain A: E.287, D.382, S.385 Ligands: ATP.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.287, A:D.382, A:D.382, H2O.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hagelueken, G. et al., Structure of Wbdd; a Bifunctional Kinase and Methyltransferase that Regulates the Chain Length of the O Antigen in Escherichia Coli O9A. Mol.Microbiol. (2012)

Release Date

2012-09-26

Peptides

WBDD: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

WBDD