SMTL ID : 4jhq.1

Crystal structure of avidin - 6-(6-biotinamidohexanamido)hexanoylferrocene complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-tetramer

Ligands

4 x B6F: [(1,2,3,4,5-eta)-cyclopentadienyl][(1,2,3,4,5-eta)-{6-[(6-{[5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanoyl]amino}hexanoyl)amino]hexanoyl}cyclopentadienyl]iron(Non-covalent)

B6F.1: 22 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, F.79, W.97, S.101, K.111, R.114, N.118 Chain C: A.39, W.110, R.114 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:T.40, A:W.70, A:W.70, A:F.72, A:K.111 Hydrogen bonds: A:N.12, A:S.16, A:Y.33, A:T.35, A:T.35, A:A.39, A:T.40, A:S.73, A:S.75, A:S.75, A:S.101, A:S.101, A:R.114, A:N.118, C:R.114 B6F.3: 17 residues within 4Å: Chain B: N.12, L.14, S.16, Y.33, T.35, A.36, W.70, F.72, S.73, S.75, T.77, F.79, W.97, L.99, N.118 Chain D: W.110, K.111 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:W.70, B:W.70, B:F.72, B:F.72, D:W.110 Hydrogen bonds: B:N.12, B:S.16, B:S.73, B:S.75, B:N.118 B6F.5: 22 residues within 4Å: Chain A: A.39, W.110, R.114 Chain C: 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, F.79, W.97, S.101, K.111, R.114, N.118 20 PLIP interactions: 19 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:T.40, C:W.70, C:W.70, C:F.72, C:K.111 Hydrogen bonds: C:N.12, C:S.16, C:Y.33, C:T.35, C:T.35, C:A.39, C:T.40, C:S.73, C:S.75, C:S.75, C:S.101, C:S.101, C:R.114, C:N.118, A:R.114 B6F.7: 17 residues within 4Å: Chain B: W.110, K.111 Chain D: N.12, L.14, S.16, Y.33, T.35, A.36, W.70, F.72, S.73, S.75, T.77, F.79, W.97, L.99, N.118 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:W.70, D:W.70, D:F.72, D:F.72, B:W.110 Hydrogen bonds: D:N.12, D:S.16, D:S.73, D:S.75, D:N.118

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 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.34 Hydrogen bonds: A:G.15 NAG.4: 7 residues within 4Å: Chain B: G.15, N.17, T.34, T.35, A.36, 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.6: 4 residues within 4Å: Chain C: G.15, N.17, T.34, L.123 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:T.34 Hydrogen bonds: C:G.15 NAG.8: 7 residues within 4Å: Chain D: G.15, N.17, T.34, T.35, A.36, 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Plazuk, D. et al., Ferrocene-Biotin Conjugates Targeting Cancer Cells: Synthesis, Interaction with Avidin, Cytotoxic Properties and the Crystal Structure of the Complex of Avidin with a Biotin-Linker-Ferrocene Conjugate. Organometallics (2013)

Release Date

2013-11-20

Peptides

Avidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Avidin

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