SMTL ID : 8ck7.1

Avidin complexed to theophylline

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: A.1, R.2, K.3 Ligands: SO4.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.2, A:K.3 GOL.8: 4 residues within 4Å: Chain C: A.1, R.2, K.3 Ligands: SO4.12 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.2, C:K.3

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

NAG.2: 4 residues within 4Å: Chain A: G.15, N.17, T.34, L.123 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.15, A:N.17 Water bridges: A:K.9 NAG.6: 6 residues within 4Å: Chain B: G.15, N.17, T.34, T.35, I.44, L.123 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.34, B:I.44 Hydrogen bonds: B:G.15 NAG.9: 4 residues within 4Å: Chain C: G.15, N.17, T.34, L.123 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.15, C:N.17 Water bridges: C:K.9 NAG.13: 6 residues within 4Å: Chain D: G.15, N.17, T.34, T.35, I.44, L.123 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:T.34, D:I.44 Hydrogen bonds: D:G.15

4 x TEP: THEOPHYLLINE(Non-covalent)

TEP.3: 11 residues within 4Å: Chain A: L.14, T.35, V.37, T.38, W.70, T.77, F.79, W.97, L.99, N.118 Chain C: W.110 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A pi-Stacking: C:W.110, C:W.110 Hydrogen bonds: A:V.37, A:T.77 Water bridges: A:T.38 TEP.7: 8 residues within 4Å: Chain B: L.14, W.70, T.77, F.79, W.97, L.99, N.118 Chain D: W.110 2 PLIP interactions: 2 interactions with chain D pi-Stacking: D:W.110, D:W.110 TEP.10: 11 residues within 4Å: Chain A: W.110 Chain C: L.14, T.35, V.37, T.38, W.70, T.77, F.79, W.97, L.99, N.118 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:V.37, C:T.77 Water bridges: C:T.38 pi-Stacking: A:W.110, A:W.110 TEP.14: 8 residues within 4Å: Chain B: W.110 Chain D: L.14, W.70, T.77, F.79, W.97, L.99, N.118 2 PLIP interactions: 2 interactions with chain B pi-Stacking: B:W.110, B:W.110

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 5 residues within 4Å: Chain A: R.2, K.90, E.91, R.122, R.124 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.91, A:E.91 Salt bridges: A:R.2, A:K.90, A:R.124 SO4.5: 3 residues within 4Å: Chain A: A.1, R.2 Ligands: GOL.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.1 SO4.11: 5 residues within 4Å: Chain C: R.2, K.90, E.91, R.122, R.124 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.91, C:E.91 Salt bridges: C:R.2, C:K.90, C:R.124 SO4.12: 3 residues within 4Å: Chain C: A.1, R.2 Ligands: GOL.8 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Spinello, A. et al., The avidin-theophylline complex: A structural and computational study. Proteins (2023)

Release Date

2023-12-27

Peptides

Avidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Avidin