SMTL ID : 4tzu.1 (1 other biounit)

Crystal Structure of Murine Cereblon in Complex with Pomalidomide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 8 residues within 4Å: Chain A: K.46, K.83, K.95, W.97 Chain C: S.92, P.93, Q.94 Ligands: SO4.6 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain C Water bridges: A:K.46, A:K.46, A:K.46, C:K.95 Salt bridges: A:K.46, A:K.83, A:K.95, C:K.95 Hydrogen bonds: C:Q.94 SO4.2: 7 residues within 4Å: Chain A: P.93, Q.94 Chain B: K.46, K.83, K.95, W.97 Ligands: SO4.6 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.94, A:K.95 Water bridges: B:W.97 Salt bridges: B:K.46, B:K.83 SO4.5: 7 residues within 4Å: Chain B: P.93, Q.94, K.95 Chain C: K.46, K.83, K.95 Ligands: SO4.6 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain B Water bridges: C:K.83, B:M.91 Salt bridges: C:K.46, C:K.83, C:K.95, B:K.95 Hydrogen bonds: B:Q.94, B:K.95 SO4.6: 9 residues within 4Å: Chain A: K.46, K.95 Chain B: K.46, K.95 Chain C: K.46, K.95 Ligands: SO4.1, SO4.2, SO4.5 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 2 interactions with chain B Salt bridges: A:K.46, A:K.95, C:K.46, C:K.95, B:K.46, B:K.95 SO4.7: 1 residues within 4Å: Chain B: H.60 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.60 Salt bridges: B:H.60 SO4.10: 1 residues within 4Å: Chain C: H.60 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:H.60

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.5, C.8, C.73, C.76 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.5, A:C.8, A:C.73, A:C.76 ZN.8: 4 residues within 4Å: Chain B: C.5, C.8, C.73, C.76 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.5, B:C.8, B:C.73, B:C.76 ZN.11: 4 residues within 4Å: Chain C: C.5, C.8, C.73, C.76 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.5, C:C.8, C:C.73, C:C.76

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

Y70.4: 7 residues within 4Å: Chain A: V.59, H.60, S.61, W.62, W.68, W.82, F.84 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.62, A:W.68, A:W.68, A:W.82 Hydrogen bonds: A:H.60, A:W.62 Y70.9: 7 residues within 4Å: Chain B: V.59, H.60, S.61, W.62, W.68, W.82, F.84 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.68, B:W.68, B:W.82 Hydrogen bonds: B:H.60, B:W.62 Y70.12: 7 residues within 4Å: Chain C: V.59, H.60, S.61, W.62, W.68, W.82, F.84 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.62, C:W.68, C:W.68, C:W.82 Hydrogen bonds: C:H.60, C:W.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chamberlain, P.P. et al., Structural Basis for Responsiveness to Thalidomide-Analog Drugs Defined by the Crystal Structure of the Human Cereblon:DDB1:Lenalidomide Complex. to be published

Release Date

2014-08-06

Peptides

Protein cereblon: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

Protein cereblon

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