SMTL ID : 2a5c.1

Structure of Avidin in complex with the ligand 8-oxodeoxyadenosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.36, A:I.44 Hydrogen bonds: A:G.15, A:N.17 NAG.3: 5 residues within 4Å: Chain B: G.15, N.17, T.34, I.44, L.123 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.44 Hydrogen bonds: B:G.15, B:N.17 NAG.5: 7 residues within 4Å: Chain C: G.15, N.17, T.34, T.35, A.36, I.44, L.123 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.36, C:I.44 Hydrogen bonds: C:G.15, C:N.17 NAG.7: 5 residues within 4Å: Chain D: G.15, N.17, T.34, I.44, L.123 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.44 Hydrogen bonds: D:G.15, D:N.17

4 x 8DA: 8-OXODEOXYADENOSINE(Non-covalent)

8DA.2: 10 residues within 4Å: Chain A: L.14, Y.33, W.70, F.72, T.77, F.79, W.97, L.99, N.118 Chain C: W.110 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.14, C:W.110 Hydrogen bonds: A:N.12, A:T.77, A:T.77, A:N.118, A:N.118 Water bridges: A:A.36 pi-Stacking: A:W.70 8DA.4: 11 residues within 4Å: Chain B: L.14, Y.33, T.35, A.36, W.70, F.72, T.77, F.79, W.97, N.118 Chain D: W.110 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.14 Hydrogen bonds: B:Y.33, B:T.35, B:A.36, B:N.118 pi-Stacking: B:W.70, B:W.70 8DA.6: 10 residues within 4Å: Chain A: W.110 Chain C: L.14, Y.33, W.70, F.72, T.77, F.79, W.97, L.99, N.118 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.14, A:W.110 Hydrogen bonds: C:N.12, C:T.77, C:T.77, C:N.118, C:N.118 Water bridges: C:A.36 pi-Stacking: C:W.70 8DA.8: 11 residues within 4Å: Chain B: W.110 Chain D: L.14, Y.33, T.35, A.36, W.70, F.72, T.77, F.79, W.97, N.118 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:L.14 Hydrogen bonds: D:Y.33, D:T.35, D:A.36, D:N.118 pi-Stacking: D:W.70, D:W.70

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