SMTL ID : 5yj1.8 (15 other biounits)

Mouse Cereblon thalidomide binding domain complexed with R-form thalidomide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x 6EL: 2-[(3~{R})-2,6-bis(oxidanylidene)piperidin-3-yl]isoindole-1,3-dione(Non-covalent)

6EL.1: 7 residues within 4Å: Chain A: V.61, H.62, S.63, W.64, W.70, W.84, F.86 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.64, A:W.70, A:W.84, A:W.84 Hydrogen bonds: A:H.62, A:W.64

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.7, C.10, C.75, C.78 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.7, A:C.10, A:C.75, A:C.78

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain A: K.48, K.97 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.48, A:K.97 SO4.4: 1 residues within 4Å: Chain A: H.62 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.62 Salt bridges: A:H.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mori, T. et al., Structural basis of thalidomide enantiomer binding to cereblon. Sci Rep (2018)

Release Date

2018-02-07

Peptides

Protein cereblon: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
V

Protein cereblon

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