SMTL ID : 6q0r.1

Structure of DDB1-DDA1-DCAF15 complex bound to E7820 and RBM39

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-1-1-1-mer

Ligands

1 x OXM: OXAMIC ACID(Non-covalent)

OXM.1: 7 residues within 4Å: Chain B: Y.238, P.245, T.246, Q.252, L.260, L.261, N.262 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.238, B:Y.238, B:N.262, B:N.262

1 x O6M: 3-cyano-N-(3-cyano-4-methyl-1H-indol-7-yl)benzene-1-sulfonamide(Non-covalent)

O6M.2: 15 residues within 4Å: Chain B: T.246, F.247, Q.248, P.249, A.250, F.251 Chain C: V.140, R.215, C.218, V.219, V.222 Chain D: N.35, T.37, D.39, M.40 13 PLIP interactions: 2 interactions with chain D, 8 interactions with chain B, 3 interactions with chain C Water bridges: D:D.39, D:D.39 Hydrophobic interactions: B:T.246, B:A.250, B:F.251, C:V.140, C:V.219, C:V.222 Hydrogen bonds: B:F.247, B:F.247, B:A.250, B:F.251 pi-Stacking: B:F.251

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain B: C.209, C.212, C.227, H.230 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.209, B:C.212, B:C.227, B:H.230

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Faust, T.B. et al., Structural complementarity facilitates E7820-mediated degradation of RBM39 by DCAF15. Nat.Chem.Biol. (2020)

Release Date

2019-11-13

Peptides

DNA damage-binding protein 1: A
DDB1- and CUL4-associated factor 15: B
DDB1- and CUL4-associated factor 15: C
RNA-binding protein 39: D
DET1- and DDB1-associated protein 1: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

DNA damage-binding protein 1

DDB1- and CUL4-associated factor 15

DDB1- and CUL4-associated factor 15

RNA-binding protein 39

DET1- and DDB1-associated protein 1

Related Entries With Identical Sequence