SMTL ID : 6h0f.4 (3 other biounits)

Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain B: C.307, Q.309, C.310, C.375, I.377, C.378 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.307, B:C.310, B:C.375, B:C.378 ZN.3: 6 residues within 4Å: Chain C: C.11, Q.13, C.14, A.16, H.27, H.31 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.11, C:C.14, C:H.27, C:H.31

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

Y70.2: 17 residues within 4Å: Chain B: N.335, P.336, H.337, H.341, E.361, H.362, S.363, W.364, W.370, W.384, F.386 Chain C: Q.10, C.11, N.12, Q.13, C.14, G.15 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:W.364, B:W.370, B:W.370, B:W.370, B:W.384 Hydrogen bonds: B:N.335, B:E.361, B:H.362, B:H.362, B:W.364, C:Q.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sievers, Q.L. et al., Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN. Science (2018)

Release Date

2018-11-07

Peptides

DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1: A
Protein cereblon: B
DNA-binding protein Ikaros: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

B
K

C
L

DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1

Protein cereblon

DNA-binding protein Ikaros

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