SMTL ID : 2dem.1

Crystal structure of Uracil-DNA glycosylase in complex with AP:A containing DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

2 x 2HP: DIHYDROGENPHOSPHATE ION(Non-covalent)

2HP.1: 3 residues within 4Å: Chain B: C.13, A.14 Chain C: R.31 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.31 2HP.3: 10 residues within 4Å: Chain A: X.8 Chain C: A.59, P.60, G.61, G.64, S.65, P.71, F.72, D.75, S.77 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.61, C:S.65, C:S.65, C:F.72 Water bridges: C:A.59

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.2: 12 residues within 4Å: Chain C: L.10, C.13, L.15, C.16, L.19, P.42, V.113, R.114, C.115, A.129, C.130, W.133 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.13, C:C.16, C:C.115, C:C.130

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain C: F.72, T.73, G.74, D.75, E.95, S.96 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.74, C:D.75, C:A.79, C:E.95, C:S.96 GOL.5: 2 residues within 4Å: Chain C: P.37, Y.38 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.38, C:Y.38

1 x EOH: ETHANOL(Non-functional Binders)

EOH.6: 2 residues within 4Å: Chain C: T.202, R.203 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:R.203 Hydrogen bonds: C:R.203 Water bridges: C:L.201, C:E.204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kosaka, H. et al., Crystal structure of family 5 uracil-DNA glycosylase bound to DNA. J.Mol.Biol. (2007)

Release Date

2007-04-24

Peptides

uracil-DNA glycosylase: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

uracil-DNA glycosylase

Related Entries With Identical Sequence