SMTL ID : 6uml.1

Structural Basis for Thalidomide Teratogenicity Revealed by the Cereblon-DDB1-SALL4-Pomalidomide Complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.58 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain B: C.287, C.290, C.355, C.358 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.287, B:C.290, B:C.355, B:C.358 ZN.3: 4 residues within 4Å: Chain C: C.8, C.11, H.24, H.28 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.8, C:C.11, C:H.24, C:H.28

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

Y70.2: 16 residues within 4Å: Chain B: V.314, N.315, P.316, H.317, E.341, H.342, S.343, W.344, W.350, W.364, F.366 Chain C: V.7, C.8, V.10, C.11, G.12 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:N.315, B:W.344, B:W.350, B:W.350, B:W.350, B:W.364, B:F.366, C:V.7 Hydrogen bonds: B:N.315, B:E.341, B:H.342, B:H.342, B:W.344

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matyskiela, M.E. et al., Crystal structure of the SALL4-pomalidomide-cereblon-DDB1 complex. Nat.Struct.Mol.Biol. (2020)

Release Date

2020-04-15

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

DNA damage-binding protein 1

Protein cereblon

Sal-like protein 4

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