SMTL ID : 1yf3.1

T4Dam in Complex with AdoHcy and 13-mer Oligonucleotide Making Non- and Semi-specific (~1/4) Contact

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

homo-dimer

Ligands

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 21 residues within 4Å: Chain C: Y.7, N.10, K.11, L.31, F.32, C.33, G.34, G.35, S.37, V.38, N.49, D.50, I.51, Q.52, L.155, H.156, F.157, D.171, P.173, Y.181, F.184 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:Y.7, C:K.11, C:G.35, C:S.37, C:I.51, C:Q.52, C:Q.52, C:H.156, C:F.157, C:D.171, C:D.171 Water bridges: C:L.36, C:V.38 SAH.3: 24 residues within 4Å: Chain D: Y.7, G.9, N.10, K.11, L.31, F.32, C.33, G.34, G.35, L.36, S.37, N.49, D.50, I.51, Q.52, L.155, H.156, F.157, D.171, P.173, Y.181, F.184, W.185, E.189 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:Y.7, D:K.11, D:F.32, D:G.35, D:L.36, D:S.37, D:I.51, D:Q.52, D:H.156, D:F.157, D:D.171 Water bridges: D:V.38, D:V.38, D:E.189

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain C: Y.7, T.8, Q.52, M.114, I.115, Y.181 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.7, C:T.8, C:T.8, C:Q.52, C:I.115 GOL.4: 6 residues within 4Å: Chain D: Y.7, T.8, Q.52, M.114, I.115, Y.181 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.8, D:Q.52, D:I.115, D:I.115 Water bridges: D:D.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horton, J.R. et al., Transition from Nonspecific to Specific DNA Interactions along the Substrate-Recognition Pathway of Dam Methyltransferase. Cell(Cambridge,Mass.) (2005)

Release Date

2005-05-17

Peptides

DNA adenine methylase: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

DNA adenine methylase