SMTL ID : 8tnr.1

Cryo-EM structure of DDB1dB:CRBN:PT-179:SD40, conformation 2

Coordinates

PDB Format Compare

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 B: C.366, Q.368, C.369, C.434, I.436, C.437 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.366, B:C.369, B:C.434, B: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 MIQ: 2-[(3S)-2,6-dioxopiperidin-3-yl]-5-(morpholin-4-yl)-1H-isoindole-1,3(2H)-dione(Non-covalent)

MIQ.2: 18 residues within 4Å: Chain B: V.393, 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 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:P.395, B:W.423, B:W.429 Hydrogen bonds: B:N.394, B:H.400, B:H.421, B:H.421, B:W.423, B: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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

DNA damage-binding protein 1

Protein cereblon

Maltose/maltodextrin-binding periplasmic protein,SD40

Related Entries With Identical Sequence