SMTL ID : 8u15.1 (1 other biounit)

The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to CC-220

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 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 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.254, A:C.257, A:C.322, A:C.325 ZN.8: 4 residues within 4Å: Chain C: C.7, C.10, H.23, H.27 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.7, C:C.10, C:H.23, C:H.27 ZN.9: 4 residues within 4Å: Chain C: C.35, C.38, H.51, H.55 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.35, C:C.38, C:H.51, C:H.55

1 x 8W7: (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione(Non-covalent)

8W7.2: 17 residues within 4Å: Chain A: N.282, P.283, H.284, E.308, H.309, S.310, W.311, W.317, W.331, F.333 Chain C: K.12, V.34, C.35, S.36, V.37, C.38, G.39 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:P.283, A:E.308, A:W.311, A:W.317, A:W.317, A:W.317, A:W.331, A:F.333, C:V.34 Hydrogen bonds: A:N.282, A:H.309, A:W.311

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

SO4.3: 3 residues within 4Å: Chain A: R.187, Q.191, N.247 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.187, A:Q.191, A:N.247, B:E.538 Salt bridges: A:R.187 SO4.4: 6 residues within 4Å: Chain A: H.288, H.328, T.349, S.351, A.352 Chain C: H.55 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Water bridges: A:S.351 Salt bridges: A:H.288, A:H.328, C:H.55 SO4.5: 1 residues within 4Å: Chain A: R.76 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.76 SO4.6: 4 residues within 4Å: Chain B: K.560, L.595, R.596, T.597 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.597, B:T.597 Salt bridges: B:K.560 SO4.7: 7 residues within 4Å: Chain B: G.56, M.57, Y.58, I.758, K.759, S.760, V.761 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.56, B:V.761 SO4.10: 4 residues within 4Å: Chain C: R.31, F.42, T.43, N.47 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.43, C:N.47 Salt bridges: C:R.31

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
DDB1: B
Sal-like protein 4: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Protein cereblon

DDB1

Sal-like protein 4

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