SMTL ID : 4ax8.1

Medium resolution structure of the bifunctional kinase- methyltransferase WbdD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

monomer

Ligands

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

SAM.1: 23 residues within 4Å: Chain A: Y.29, Q.30, R.49, L.73, G.74, C.75, A.76, F.80, I.94, D.95, F.96, Q.97, N.100, G.121, R.122, I.123, E.124, L.141, S.142, V.143, H.145, H.146, I.147 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.29, A:A.76 Hydrogen bonds: A:Y.29, A:Q.30, A:G.74, A:A.76, A:D.95, A:D.95, A:F.96, A:Q.97, A:N.100, A:I.123, A:E.124 Salt bridges: A:R.49 pi-Stacking: A:F.96, A:F.96 pi-Cation interactions: A:Y.29

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 9 residues within 4Å: Chain A: R.44, D.45, C.46, N.47, Q.48, R.49, L.50, F.207, D.208 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.45, A:C.46, A:Q.48, A:R.49 Salt bridges: A:R.44, A:R.49 SO4.3: 2 residues within 4Å: Chain A: S.347, R.350 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.350, A:H.377

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

ADP.4: 20 residues within 4Å: Chain A: Q.239, P.242, Y.243, R.254, Y.256, F.258, V.263, K.265, F.267, E.287, P.305, M.321, E.322, K.323, L.324, L.328, W.368, M.371, I.381, D.382 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:P.242, A:P.242, A:Y.256, A:E.287, A:E.322, A:L.324, A:D.382 Salt bridges: A:R.254, A:K.265, A:K.265

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

CL.5: 7 residues within 4Å: Chain A: S.142, V.143, F.144, H.145, E.173, L.174, A.175 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hagelueken, G. et al., Crystallization, Dehydration and Experimental Phasing of Wbdd, a Bifunctional Kinase and Methyltransferase from Escherichia Coli O9A. Acta Crystallogr.,Sect.D (2012)

Release Date

2012-10-03

Peptides

WBDD: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

WBDD