SMTL ID : 5myq.1

Crystal structure of avidin in complex with ferrocene homobiotin derivative

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-tetramer

Ligands

4 x HBF: ferrocene homobiotin derivative(Non-covalent)

HBF.1: 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, W.97, L.99, S.101, R.114, N.118 Chain C: W.110 Ligands: IOD.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.35, A:W.70, A:W.70, A:F.72, A:L.99 Hydrogen bonds: A:N.12, A:S.16, A:Y.33, A:T.35, A:N.118, A:N.118 HBF.7: 22 residues within 4Å: Chain B: N.12, L.14, S.16, Y.33, T.35, V.37, T.38, A.39, 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, K.111 Ligands: IOD.10 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.70, B:F.72, B:F.72 Hydrogen bonds: B:N.12, B:S.16, B:T.35, B:T.35, B:N.118, B:N.118 HBF.15: 22 residues within 4Å: Chain A: W.110, K.111 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 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:W.70, C:F.72 Hydrogen bonds: C:N.12, C:S.16, C:Y.33, C:T.35, C:T.35, C:N.118, C:N.118 HBF.22: 22 residues within 4Å: Chain B: W.110, K.111 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 Ligands: IOD.25 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:W.70, D:W.70, D:W.70, D:F.72, D:F.72, D:L.99 Hydrogen bonds: D:N.12, D:S.16, D:T.35, D:N.118, D:N.118

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

NAG.2: 7 residues within 4Å: Chain A: K.9, G.15, N.17, T.34, T.35, A.36, L.123 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.36 Hydrogen bonds: A:K.9, A:G.15 Water bridges: A:N.17, A:N.17 NAG.8: 5 residues within 4Å: Chain B: K.9, G.15, N.17, T.34, L.123 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.34 Hydrogen bonds: B:K.9, B:G.15 NAG.16: 3 residues within 4Å: Chain C: G.15, N.17, T.34 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.34 Hydrogen bonds: C:G.15 Water bridges: C:N.17 NAG.23: 5 residues within 4Å: Chain D: K.9, G.15, N.17, T.34, L.123 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:T.34 Hydrogen bonds: D:K.9, D:G.15

21 x IOD: IODIDE ION(Non-functional Binders)

IOD.3: 2 residues within 4Å: Chain A: S.102 Ligands: HBF.1 Ligand excluded by PLIP IOD.4: 4 residues within 4Å: Chain A: G.89, K.90, E.91, R.122 Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain A: K.9, R.122 Ligand excluded by PLIP IOD.6: 4 residues within 4Å: Chain A: T.32, E.46, S.47, P.48 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain B: R.2, E.91 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain B: S.102 Ligands: HBF.7 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain B: K.111 Chain D: R.114 Ligand excluded by PLIP IOD.12: 5 residues within 4Å: Chain B: N.17, M.18, T.19, T.32, T.34 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain B: T.32, S.47, P.48 Ligand excluded by PLIP IOD.14: 1 residues within 4Å: Chain B: R.2 Ligand excluded by PLIP IOD.17: 2 residues within 4Å: Chain A: K.111 Chain C: R.114 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain A: R.114 Chain C: K.111 Ligand excluded by PLIP IOD.19: 1 residues within 4Å: Chain C: S.102 Ligand excluded by PLIP IOD.20: 4 residues within 4Å: Chain C: T.32, E.46, S.47, P.48 Ligand excluded by PLIP IOD.21: 2 residues within 4Å: Chain C: K.9, R.122 Ligand excluded by PLIP IOD.24: 2 residues within 4Å: Chain B: R.114 Chain D: K.111 Ligand excluded by PLIP IOD.25: 4 residues within 4Å: Chain D: S.75, S.101, S.102 Ligands: HBF.22 Ligand excluded by PLIP IOD.26: 1 residues within 4Å: Chain D: R.2 Ligand excluded by PLIP IOD.27: 4 residues within 4Å: Chain D: M.18, T.19, T.32, T.34 Ligand excluded by PLIP IOD.28: 2 residues within 4Å: Chain D: R.2, E.91 Ligand excluded by PLIP IOD.29: 3 residues within 4Å: Chain D: E.46, S.47, P.48 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Strzelczyk, P. et al., Structural investigation of the interactions of ferrocene homobiotin derivative with avidin. To Be Published

Release Date

2018-02-14

Peptides

Avidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Avidin

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