SMTL ID : 8u17.2 (1 other biounit)

The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-long bound to Pomalidomide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-1-1-1-mer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.254, C.257, C.322, C.325 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.257, A:C.322, A:C.325 ZN.3: 4 residues within 4Å: Chain C: C.16, C.19, H.32, H.36 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.16, C:C.19, C:H.32, C:H.36 ZN.4: 4 residues within 4Å: Chain C: C.44, C.47, H.60, H.64 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.44, C:C.47, C:H.60, C:H.64

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

Y70.2: 14 residues within 4Å: Chain A: V.281, N.282, P.283, H.284, E.308, H.309, S.310, W.311, W.317, W.331 Chain C: V.43, C.44, V.46, G.48 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:W.311, A:W.317, A:W.331, C:V.43 Hydrogen bonds: A:N.282, A:H.309, A:W.311

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ma, X. et al., Structural and biophysical comparisons of the pomalidomide- and CC-220-induced interactions of SALL4 with cereblon. Sci Rep (2023)

Release Date

2023-12-27

Peptides

Protein cereblon: A
DNA damage-binding protein 1: B
Sal-like protein 4: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Protein cereblon

DNA damage-binding protein 1

Sal-like protein 4

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