SMTL ID : 9gh7.1

Complex of human TfR1 with a potent bicyclic peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

hetero-2-2-mer

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: F.105, N.235, E.301 Chain C: W.559 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.105 NAG-NAG.2: 3 residues within 4Å: Chain A: N.645, T.647, L.648 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: W.559 Chain C: F.105, N.235, E.301 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.105 NAG-NAG.7: 3 residues within 4Å: Chain C: N.645, T.647, L.648 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: T.228, F.231, E.383, E.386 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.228, A:T.228, A:F.231, A:E.383, A:E.386 CA.8: 4 residues within 4Å: Chain C: T.228, F.231, E.383, E.386 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:T.228, C:T.228, C:F.231, C:E.383, C:E.386

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: S.97, K.312, G.313, F.314 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.97, A:S.97, A:K.312, A:G.313 GOL.9: 4 residues within 4Å: Chain C: S.97, K.312, G.313, F.314 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.97, C:S.97, C:K.312, C:G.313

2 x 01: 1-(3,5-diethanoyl-1,3,5-triazinan-1-yl)ethanone

01.5: 12 residues within 4Å: Chain A: P.72, E.74, W.330, G.331, P.332, T.487 Chain B: C.2, A.6, G.9, C.10, S.12, C.14 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.6 Hydrogen bonds: A:G.331 01.10: 12 residues within 4Å: Chain C: P.72, E.74, W.330, G.331, P.332, T.487 Chain D: C.2, A.6, G.9, C.10, S.12, C.14 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.331 Hydrophobic interactions: D:A.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ostergaard, M.E. et al., Conjugation to a transferrin receptor 1-binding Bicycle peptide enhances ASO and siRNA potency in skeletal and cardiac muscles. Nucleic Acids Res. (2025)

Release Date

2025-04-30

Peptides

Transferrin receptor protein 1: AC
Bicyclic peptide: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
P

D
P

Transferrin receptor protein 1

Bicyclic peptide