SMTL ID : 6en4.1

SF3b core in complex with a splicing modulator

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.08 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain D: C.40, C.43, C.82, C.85 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.40, D:C.43, D:C.82, D:C.85 ZN.2: 4 residues within 4Å: Chain D: C.33, C.36, C.68, C.71 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.33, D:C.68, D:C.71 ZN.3: 4 residues within 4Å: Chain D: C.21, C.56, C.59, C.95 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.21, D:C.56, D:C.59, D:C.95

1 x BGZ: [(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~{E},6~{S})-6-methyl-7-[(2~{R},3~{R})-3-[(2~{R},3~{S})-3-oxidanylpentan-2-yl]oxiran-2-yl]hepta-2,4-dien-2-yl]-7,10-bis(oxidanyl)-12-oxidanylidene-1-oxacyclododec-4-en-6-yl] ethanoate(Non-covalent)

BGZ.4: 12 residues within 4Å: Chain C: L.614, K.619, R.622, R.623, V.626, V.658, V.662, F.701, Y.705 Chain D: Y.46, V.47, R.48 12 PLIP interactions: 4 interactions with chain D, 8 interactions with chain C Hydrophobic interactions: D:Y.46, D:Y.46, C:K.619, C:V.626, C:V.662, C:F.701, C:F.701, C:Y.705 Hydrogen bonds: D:Y.46, D:R.48, C:R.623 Salt bridges: C:R.622

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cretu, C. et al., Structural Basis of Splicing Modulation by Antitumor Macrolide Compounds. Mol. Cell (2018)

Release Date

2018-06-20

Peptides

Splicing factor 3B subunit 3: A
Splicing factor 3B subunit 5: B
Splicing factor 3B subunit 1: C
PHD finger-like domain-containing protein 5A: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Splicing factor 3B subunit 3

Splicing factor 3B subunit 5

Splicing factor 3B subunit 1

PHD finger-like domain-containing protein 5A

Related Entries With Identical Sequence