SMTL ID : 5irw.1

Crystal structure of avidin in complex with 1-desthiobiotinylpyrene

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: K.9, G.15, N.17, T.34, L.123 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.9, A:G.15, A:N.17 NAG.3: 6 residues within 4Å: Chain B: K.9, G.15, N.17, T.34, A.36, L.123 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.36 Hydrogen bonds: B:K.9, B:G.15, B:N.17 NAG.5: 5 residues within 4Å: Chain C: G.15, N.17, T.34, A.36, L.123 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:T.34, C:A.36 Hydrogen bonds: C:K.9, C:G.15, C:N.17 NAG.7: 6 residues within 4Å: Chain D: K.9, G.15, N.17, T.34, A.36, L.123 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:A.36 Hydrogen bonds: D:K.9, D:G.15, D:N.17

4 x D9P: 1-desthiobiotinylpyrene(Non-covalent)

D9P.2: 18 residues within 4Å: Chain A: N.12, S.16, Y.33, T.35, V.37, T.38, A.39, T.40, W.70, F.72, S.73, S.75, T.77, W.97, L.99, S.101, N.118 Chain C: W.110 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:T.38, A:A.39, A:T.40, A:W.70, A:F.72, A:T.77, A:W.97, A:L.99, C:W.110 Hydrogen bonds: A:N.12, A:S.16, A:T.35, A:T.35, A:A.39, A:T.40, A:N.118 D9P.4: 18 residues within 4Å: Chain B: N.12, S.16, Y.33, T.35, V.37, T.38, A.39, T.40, W.70, F.72, S.75, T.77, F.79, W.97, L.99, S.101, N.118 Chain D: W.110 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:W.70, B:F.72, B:T.77, B:F.79, B:W.97, B:L.99, D:W.110, D:W.110 Hydrogen bonds: B:N.12, B:S.16, B:Y.33, B:T.35, B:T.35, B:A.39, B:T.40, B:N.118 D9P.6: 20 residues within 4Å: Chain A: W.110 Chain C: N.12, L.14, S.16, Y.33, T.35, V.37, T.38, A.39, T.40, W.70, F.72, S.73, S.75, T.77, F.79, W.97, S.101, R.114, N.118 14 PLIP interactions: 1 interactions with chain A, 13 interactions with chain C Hydrophobic interactions: A:W.110, C:A.39, C:W.70, C:F.72, C:T.77, C:F.79, C:W.97 Hydrogen bonds: C:N.12, C:S.16, C:T.35, C:T.35, C:T.38, C:A.39, C:N.118 D9P.8: 18 residues within 4Å: Chain B: W.110 Chain D: N.12, L.14, S.16, Y.33, T.35, V.37, T.38, A.39, T.40, W.70, S.73, S.75, F.79, W.97, S.101, R.114, N.118 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:A.39, D:T.40, D:W.70, D:F.79, D:W.97, B:W.110 Hydrogen bonds: D:N.12, D:S.16, D:Y.33, D:T.35, D:T.38, D:A.39, D:T.40, D:N.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Strzelczyk, P. et al., Structural Characterization of the Avidin Interactions with Fluorescent Pyrene-Conjugates: 1-Biotinylpyrene and 1-Desthiobiotinylpyrene. Molecules (2016)

Release Date

2016-10-12

Peptides

Avidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Avidin

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