SMTL ID : 2a8g.1

Structure of Avidin in complex with the ligand deoxyguanosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 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.13, N.15, T.32, T.33, A.34, I.42, L.121 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.13, A:N.15 NAG.2: 7 residues within 4Å: Chain B: G.13, N.15, T.32, T.33, A.34, I.42, L.121 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.34 Hydrogen bonds: B:G.13, B:N.15 NAG.4: 7 residues within 4Å: Chain C: G.13, N.15, T.32, T.33, A.34, I.42, L.121 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.13, C:N.15 NAG.5: 7 residues within 4Å: Chain D: G.13, N.15, T.32, T.33, A.34, I.42, L.121 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:A.34 Hydrogen bonds: D:G.13, D:N.15

2 x GNG: 2'-DEOXY-GUANOSINE(Non-covalent)

GNG.3: 12 residues within 4Å: Chain B: N.10, S.14, Y.31, W.68, F.70, S.71, S.73, T.75, F.77, W.95, L.97, N.116 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.10, B:S.14, B:S.14, B:Y.31, B:S.71, B:S.73, B:S.73, B:N.116 pi-Stacking: B:W.95, B:W.95, B:W.95 GNG.6: 12 residues within 4Å: Chain D: N.10, S.14, Y.31, W.68, F.70, S.71, S.73, T.75, F.77, W.95, L.97, N.116 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:N.10, D:S.14, D:S.14, D:Y.31, D:S.71, D:S.73, D:S.73, D:N.116 pi-Stacking: D:W.95, D:W.95, D:W.95

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