SMTL ID : 2ddg.1

Crystal structure of uracil-DNA glycosylase in complex with AP:G containing DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 5 residues within 4Å: Chain A: T.5, G.6 Chain B: A.12, C.13 Chain C: K.30 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.30 ACT.3: 3 residues within 4Å: Chain C: H.161, F.162, R.183 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.183 Salt bridges: C:H.161, C:R.183

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

2HP.2: 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.5: 9 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 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)

SF4.4: 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

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 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

4 x EOH: ETHANOL(Non-functional Binders)

EOH.7: 2 residues within 4Å: Chain C: T.202, R.203 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.203 Water bridges: C:E.204 EOH.8: 2 residues within 4Å: Chain C: R.128, A.131 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:R.128 EOH.9: 3 residues within 4Å: Chain C: R.132, W.133, V.136 No protein-ligand interaction detected (PLIP) EOH.10: 3 residues within 4Å: Chain A: C.7 Chain C: R.29, H.63 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.63

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

2007-02-13

Peptides

uracil-DNA glycosylase: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

uracil-DNA glycosylase

Related Entries With Identical Sequence