SMTL ID : 6wrx.1

Crystal structure of computationally designed protein 2DS25.1 in complex with the human Transferrin receptor ectodomain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.07 Å

Oligo State

hetero-2-2-mer

Ligands

2 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: 5 residues within 4Å: Chain A: F.67, N.197, F.201, E.263 Chain B: W.521 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 2 residues within 4Å: Chain A: 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.3: 3 residues within 4Å: Chain B: N.607, T.609, L.610 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.4: 7 residues within 4Å: Chain A: W.521 Chain B: F.67, N.197, F.201, E.263, I.264 Ligands: MAN.7 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 6 residues within 4Å: Chain A: D.187, 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:F.193, A:E.345, A:E.348 CA.8: 6 residues within 4Å: Chain B: D.187, T.190, F.193, S.195, E.345, E.348 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:T.190, B:T.190, B:F.193, B:E.345, B:E.348

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

NAG.6: 2 residues within 4Å: Chain B: N.131, G.132 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.131

1 x MAN: alpha-D-mannopyranose(Non-functional Binders)

MAN.7: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN.4 No protein-ligand interaction detected (PLIP)

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: AB
Computationally designed protein 2DS25.1: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Transferrin receptor protein 1

Computationally designed protein 2DS25.1

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