SMTL ID : 4i60.1

Crystal structure of avidin - biotinylruthenocene complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain A: K.9, G.15, N.17, L.123 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: K.9, G.15, N.17, L.123 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: K.9, G.15, N.17, L.123 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain D: K.9, G.15, N.17, L.123 No protein-ligand interaction detected (PLIP)

4 x B1R: [(1,2,3,4,5-eta)-cyclopentadienyl][(1,2,3,4,5-eta)-{5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}cyclopentadienyl]ruthenium(Non-covalent)

B1R.2: 21 residues within 4Å: Chain A: 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, L.99, S.101, R.114, N.118 Chain D: W.110 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.70, A:F.72, A:L.99 Hydrogen bonds: A:N.12, A:S.16, A:T.35, A:A.39, A:N.118 B1R.4: 21 residues within 4Å: Chain B: 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, L.99, S.101, R.114, N.118 Chain C: W.110 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.70, B:F.72, B:L.99 Hydrogen bonds: B:N.12, B:S.16, B:T.35, B:A.39, B:N.118 B1R.6: 21 residues within 4Å: Chain B: 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, L.99, S.101, R.114, N.118 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:W.70, C:F.72, C:L.99 Hydrogen bonds: C:N.12, C:S.16, C:Y.33, C:T.35, C:T.35, C:A.39, C:T.40, C:N.118 B1R.8: 21 residues within 4Å: Chain A: W.110 Chain D: 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, L.99, S.101, R.114, N.118 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:W.70, D:F.72, D:L.99 Hydrogen bonds: D:N.12, D:S.16, D:Y.33, D:T.35, D:T.35, D:A.39, D:T.40, D:N.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Strzelczyk, P. et al., Structural investigation of the interactions of biotinylruthenocene with avidin. Chem.Biol.Interact (2013)

Release Date

2013-08-14

Peptides

Avidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Avidin

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