SMTL ID : 7b91.1

Structure of a minimal SF3B core in complex with pladienolide D (form I)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x T2Z: [(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] ethanoate(Non-covalent)

T2Z.1: 11 residues within 4Å: Chain C: L.614, K.615, K.619, R.622, V.626, F.701, Y.705 Chain D: D.44, Y.46, V.47, R.48 10 PLIP interactions: 4 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:Y.46, D:Y.46, C:K.619, C:V.626, C:F.701, C:F.701, C:Y.705 Hydrogen bonds: D:D.44, D:R.48 Salt bridges: C:R.622

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain D: C.33, C.36, C.68, C.71 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.33, D:C.36, 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 ZN.4: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cretu, C. et al., Structural basis of intron selection by U2 snRNP in the presence of covalent inhibitors. Nat Commun (2021)

Release Date

2021-08-04

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

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