SMTL ID : 5zya.1

SF3b spliceosomal complex bound to E7107

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.95 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x 9B0: [(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~{E},6~{R})-6-methyl-6-oxidanyl-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] 4-cycloheptylpiperazine-1-carboxylate(Non-covalent)

9B0.1: 10 residues within 4Å: Chain B: K.1071, R.1075, V.1078, N.1108, V.1110, Y.1157, I.1158 Chain C: Y.30, V.31, R.32 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:K.1071, C:R.32 Salt bridges: B:R.1074 Hydrophobic interactions: C:Y.30

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain C: C.17, C.20, C.52, C.55 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.17, C:C.52, C:C.55 ZN.3: 4 residues within 4Å: Chain C: C.5, C.40, C.43, C.79 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.5, C:C.40, C:C.79 ZN.4: 4 residues within 4Å: Chain C: C.24, C.27, C.66, C.69 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.24, C:C.27, C:C.66, C:C.69

1 x K: POTASSIUM ION(Non-covalent)

K.5: 3 residues within 4Å: Chain D: V.611, N.613, Q.637 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Finci, L.I. et al., The cryo-EM structure of the SF3b spliceosome complex bound to a splicing modulator reveals a pre-mRNA substrate competitive mechanism of action. Genes Dev. (2018)

Release Date

2018-06-20

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

D
A

Splicing factor 3B subunit 5

Splicing factor 3B subunit 1

PHD finger-like domain-containing protein 5A

Splicing factor 3B subunit 3

Related Entries With Identical Sequence