SMTL ID : 6wrv.1

Crystal structure of computationally designed protein 3DS18 in complex with the human Transferrin receptor ectodomain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

hetero-3-3-mer

Ligands

8 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 3 residues within 4Å: Chain A: N.607, T.609, L.610 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 2 residues within 4Å: Chain A: N.131, G.132 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 5 residues within 4Å: Chain A: F.67, N.197, F.201, E.263 Chain B: W.521 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.67 NAG-NAG-BMA.5: 2 residues within 4Å: Chain B: N.131, G.132 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 5 residues within 4Å: Chain A: W.521 Chain B: F.67, N.197, F.201, E.263 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.67 NAG-NAG-BMA.7: 2 residues within 4Å: Chain C: N.131, G.132 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 4 residues within 4Å: Chain C: F.67, N.197, F.201, E.263 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.67 NAG-NAG-BMA.9: 2 residues within 4Å: Chain C: N.607, L.610 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.4: 2 residues within 4Å: Chain B: N.607, L.610 No protein-ligand interaction detected (PLIP)

3 x CA: CALCIUM ION(Non-covalent)

CA.10: 5 residues within 4Å: Chain A: T.190, F.193, S.195, E.345, E.348 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.190, A:T.190, A:E.345, A:E.345, A:E.348 CA.11: 6 residues within 4Å: Chain B: T.190, P.191, G.192, F.193, E.345, E.348 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:T.190, B:F.193, B:E.348, B:E.348 CA.12: 6 residues within 4Å: Chain C: D.187, T.190, P.191, G.192, E.345, E.348 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:T.190, C:E.345, C:E.348, C:E.348

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sahtoe, D.D. et al., Transferrin receptor targeting by de novo sheet extension. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-04-28

Peptides

Transferrin receptor protein 1: ABC
Computationally designed protein 3DS18: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
D

E
C

F
F

Transferrin receptor protein 1

Computationally designed protein 3DS18