SMTL ID : 6xnd.1

Avidin-Biotin-Phenol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

homo-tetramer

Ligands

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

NAG.1: 7 residues within 4Å: Chain A: G.15, S.16, N.17, T.34, T.35, A.36, L.123 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.36 Hydrogen bonds: A:G.15, A:N.17 NAG.3: 7 residues within 4Å: Chain B: G.15, S.16, N.17, T.34, T.35, A.36, L.123 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.15, B:N.17 NAG.5: 6 residues within 4Å: Chain C: G.15, S.16, N.17, T.34, A.36, L.123 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:A.36 Hydrogen bonds: C:G.15, C:N.17 NAG.7: 8 residues within 4Å: Chain D: K.9, G.15, S.16, N.17, T.34, T.35, A.36, L.123 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:T.34 Hydrogen bonds: D:K.9, D:N.17, D:N.17

4 x V8M: N-[2-(2-hydroxy-5-nitrophenyl)ethyl]-5-[(3aS,4S,6aS)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide(Covalent)(Non-covalent)

V8M.2: 22 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 C: W.110, R.114 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:T.40, A:W.70, A:W.70, A:F.72 Hydrogen bonds: A:N.12, A:S.16, A:Y.33, A:T.35, A:T.38, A:A.39, A:T.40, A:S.73, A:S.75, A:R.114, A:N.118, A:N.118 V8M.4: 23 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, E.74, S.75, T.77, F.79, W.97, L.99, S.101, S.102, R.114, N.118 Chain D: W.110 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:W.70, B:W.70, B:W.70, B:F.72, D:W.110 Hydrogen bonds: B:N.12, B:S.16, B:S.16, B:Y.33, B:T.38, B:A.39, B:T.40, B:S.73, B:S.75, B:W.97, B:S.101, B:S.102, B:N.118 V8M.6: 23 residues within 4Å: Chain A: 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, E.74, S.75, T.77, F.79, W.97, L.99, S.101, S.102, R.114, N.118 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:A.39, C:W.70, C:W.70, C:F.72, C:L.99 Hydrogen bonds: C:N.12, C:S.16, C:T.35, C:T.38, C:A.39, C:T.40, C:S.73, C:S.75, C:S.75, C:N.118, C:N.118 V8M.8: 23 residues within 4Å: Chain B: W.110, R.114 Chain D: N.12, L.14, S.16, Y.33, T.35, V.37, T.38, A.39, T.40, S.41, W.70, F.72, S.73, S.75, T.77, F.79, W.97, L.99, S.101, R.114, N.118 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:W.70, D:W.70, D:F.72 Hydrogen bonds: D:N.12, D:S.16, D:T.35, D:T.38, D:A.39, D:T.40, D:R.114, D:N.118, D:N.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burt, A.J. et al., A Ligand-Directed Nitrophenol Carbonate for Transient in situ Bioconjugation and Drug Delivery. Chemmedchem (2020)

Release Date

2021-03-03

Peptides

Avidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Avidin

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