SMTL ID : 8tnp.1

Cryo-EM structure of DDB1dB:CRBN:Pomalidomide:SD40

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.366, Q.368, C.369, C.434, C.437, S.439 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.366, A:C.369, A:C.434, A:C.437 ZN.3: 6 residues within 4Å: Chain C: C.424, I.426, C.427, F.429, H.440, H.444 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.424, C:C.427, C:H.440, C:H.444

1 x Y70: S-Pomalidomide(Non-covalent)

Y70.2: 17 residues within 4Å: Chain A: N.394, P.395, H.396, H.400, E.420, H.421, S.422, W.423, W.429, W.443, F.445 Chain C: F.423, C.424, P.425, I.426, C.427, G.428 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:P.395, A:W.429, A:W.443, C:F.423 Hydrogen bonds: A:N.394, A:H.421, A:W.423, A:W.429

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mercer, J.A.M. et al., Continuous evolution of compact protein degradation tags regulated by selective molecular glues. Science (2024)

Release Date

2024-03-13

Peptides

Protein cereblon: A
DNA damage-binding protein 1: B
Maltose/maltodextrin-binding periplasmic protein,SD40: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

Protein cereblon

DNA damage-binding protein 1

Maltose/maltodextrin-binding periplasmic protein,SD40

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