SMTL ID : 2a5b.1

Avidin complexed with 8-oxodeoxyguanosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

homo-tetramer

Ligands

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 7 residues within 4Å: Chain A: G.15, N.17, T.34, T.35, A.36, I.44, L.123 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.15 NAG.3: 6 residues within 4Å: Chain B: G.15, N.17, T.34, T.35, A.36, L.123 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.36 Hydrogen bonds: B:G.15, B:N.17 NAG.4: 7 residues within 4Å: Chain C: G.15, N.17, T.34, T.35, A.36, I.44, L.123 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.15 NAG.6: 6 residues within 4Å: Chain D: G.15, N.17, T.34, T.35, A.36, L.123 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:A.36 Hydrogen bonds: D:G.15, D:N.17

2 x 8HG: 2'-DEOXY-8-OXOGUANOSINE(Non-covalent)

8HG.2: 11 residues within 4Å: Chain A: L.14, T.35, W.70, F.72, S.73, S.75, T.77, W.97, L.99, N.118 Chain C: W.110 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:W.110 pi-Stacking: C:W.110, C:W.110 Hydrogen bonds: A:T.35, A:S.73, A:S.75, A:S.75, A:T.77 pi-Cation interactions: A:W.97 8HG.5: 11 residues within 4Å: Chain A: W.110 Chain C: L.14, T.35, W.70, F.72, S.73, S.75, T.77, W.97, L.99, N.118 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:T.35, C:S.73, C:S.75, C:S.75, C:T.77 pi-Cation interactions: C:W.97 Hydrophobic interactions: A:W.110 pi-Stacking: A:W.110, A:W.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Conners, R. et al., Recognition of oxidatively modified bases within the biotin-binding site of avidin. J.Mol.Biol. (2006)

Release Date

2006-05-23

Peptides

Avidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Avidin