SMTL ID : 5hlm.1

Crystal structure of avidin complex with a ferrocene biotin derivative

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x B9F: [(1,2,3,4,5-eta)-cyclopentadienyl]{(1,2,3,4,5-eta)-1-[1-hydroxy-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentyl]cyclopentadienyl}iron(Non-covalent)

B9F.1: 19 residues within 4Å: Chain A: N.12, L.14, S.16, Y.33, T.35, V.37, T.38, W.70, F.72, S.73, S.75, T.77, W.97, L.99, S.101, R.114, N.118 Chain C: W.110, K.111 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.70 Hydrogen bonds: A:N.12, A:S.16, A:T.35, A:T.35, A:S.73, A:N.118 B9F.3: 15 residues within 4Å: Chain B: N.12, L.14, S.16, Y.33, T.35, W.70, F.72, S.73, S.75, T.77, W.97, L.99, R.114, N.118 Chain D: W.110 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.70, B:F.72 Hydrogen bonds: B:N.12, B:S.16, B:Y.33, B:T.35, B:T.35, B:S.73, B:S.75, B:N.118 B9F.5: 14 residues within 4Å: Chain A: W.110 Chain C: N.12, L.14, S.16, Y.33, T.35, V.37, W.70, S.73, S.75, T.77, W.97, R.114, N.118 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:W.70 Hydrogen bonds: C:N.12, C:S.16, C:T.35, C:T.35, C:S.73, C:S.75, C:N.118 B9F.7: 20 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, F.72, S.73, S.75, T.77, 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 Hydrogen bonds: D:N.12, D:S.16, D:Y.33, D:T.35, D:T.35, D:S.73, D:S.75, D:S.75, D:N.118

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

NAG.2: 5 residues within 4Å: Chain A: K.9, G.15, N.17, I.34, L.123 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.34 Hydrogen bonds: A:K.9, A:G.15 NAG.4: 6 residues within 4Å: Chain B: K.9, G.15, N.17, I.34, T.35, A.36 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.34, B:A.36 Hydrogen bonds: B:K.9, B:G.15 NAG.6: 4 residues within 4Å: Chain C: K.9, G.15, N.17, L.123 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.9, C:G.15 NAG.8: 4 residues within 4Å: Chain D: K.9, G.15, N.17, A.36 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:A.36 Hydrogen bonds: D:K.9, D:G.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blauz, A. et al., Ferrocene-Biotin Conjugates: Synthesis, Structure, Cytotoxic Activity and Interaction with Avidin. Chempluschem (2016)

Release Date

2017-01-18

Peptides

Avidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Avidin

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