SMTL ID : 5amh.1

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide, trigonal crystal form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.25, C.28, C.91, C.94 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.25, A:C.28, A:C.91, A:C.94

1 x EF2: S-Thalidomide(Non-covalent)

EF2.2: 10 residues within 4Å: Chain A: N.51, P.52, E.77, F.78, S.79, W.80, W.86, W.100, Y.102 Ligands: CL.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.52, A:W.80, A:W.86, A:W.86, A:W.100 Hydrogen bonds: A:N.51, A:F.78, A:W.80, A:Y.102

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 2 residues within 4Å: Chain A: D.44, E.46 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.44, A:E.46, H2O.3, H2O.3, H2O.3

7 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 5 residues within 4Å: Chain A: F.57, R.58, I.115, K.116, D.117 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: I.88, H.97, W.100 Ligands: EF2.2 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: H.47, V.48 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain A: A.20, S.21, R.34, R.35, D.36 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: S.96, H.97 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: V.49, F.50, W.80 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: M.41, G.42, H.47, F.81 Ligand excluded by PLIP

1 x NI: NICKEL (II) ION(Non-covalent)

NI.11: 1 residues within 4Å: Chain A: H.45 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.45, H2O.3, H2O.3, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hartmann, M.D. et al., Structural Dynamics of the Cereblon Ligand Binding Domain. Plos One (2015)

Release Date

2015-07-01

Peptides

CEREBLON ISOFORM 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CEREBLON ISOFORM 4

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