SMTL ID : 7omf.1

Structure of a minimal SF3B core in complex with sudemycin D6 (form I)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 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.33, C.68, C.71 Ligands: SCN.5 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.33, D:C.68, D:C.71 ZN.2: 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.3: 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

1 x T2W: [(~{Z},2~{S})-5-[[4-[(2~{E},4~{E})-3-methyl-5-[(2~{S},4~{R})-4,6,6-trimethyl-4-oxidanyl-oxan-2-yl]penta-2,4-dienyl]cyclohexyl]amino]-5-oxidanylidene-pent-3-en-2-yl] ~{N}-methylcarbamate(Covalent)

T2W.4: 15 residues within 4Å: Chain C: L.614, K.615, H.617, K.619, R.622, V.626, V.658, C.659, V.662 Chain D: K.35, C.36, G.38, K.39, Y.46, I.70 11 PLIP interactions: 6 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:K.615, C:R.622, C:V.626, C:V.658, D:K.39, D:Y.46, D:I.70 Hydrogen bonds: C:L.614, C:R.622, D:K.39, D:K.39

1 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.5: 4 residues within 4Å: Chain D: C.36, I.70, C.71 Ligands: ZN.1 No protein-ligand interaction detected (PLIP)

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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