Research workbench
Structure of a minimal SF3B core in complex with spliceostatin A (form II)
Analyse Structure of a minimal SF3B core in complex with spliceostatin A (form II) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B0I
- Type
- protein
- Length
- 1,864 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3
- Source
- Homo sapiens
- Molecule
- Splicing factor 3B subunit 3,Splicing factor 3B subunit 3,Splicing factor 3B subunit 3…
- UniProt
- Q15393, Q9BWJ5, O75533, Q7RTV0
- Ligands
- SJT, ZN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · resolution 3 · 4 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Splicing factor 3B subunit 3,Splicing factor 3B subunit 3,Splicing factor 3B subunit 3 | protein | 864 | 11% helix, 47% strand | Q15393 |
| B | Splicing factor 3B subunit 5 | protein | 65 | 62% helix, 0% strand | Q9BWJ5 |
| C | Splicing factor 3B subunit 1 | protein | 842 | 78% helix, 0% strand | O75533 |
| D | PHD finger-like domain-containing protein 5A | protein | 93 | 15% helix, 26% strand | Q7RTV0 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.84 | 0.85 | 72 | empty |
| 2 | 199 | 0.81 | 0.95 | 33 | empty |
| 3 | 696 | 0.78 | 0.83 | 83 | empty |
| 4 | 1163 | 0.77 | 0.79 | 101 | empty |
| 5 | 443 | 0.70 | 0.81 | 43 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2358 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2310 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1440 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1274 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 559 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7B0I · Structure of a minimal SF3B core in complex with spliceostatin a (form II) · the same entry in another collection · chain D against D, TM-score 1.00
- Q15393 · AlphaFold monomer V2.0 prediction for splicing factor 3B subunit 3 (Q15393) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9BWJ5 · AlphaFold monomer V2.0 prediction for splicing factor 3B subunit 5 (Q9BWJ5) · a predicted model of the same protein · chain B against A, TM-score 0.92
- Q7RTV0 · AlphaFold monomer V2.0 prediction for phd finger-like domain- containing protein 5A… · a predicted model of the same protein · chain D against A, TM-score 0.88
- O75533 · AlphaFold monomer V2.0 prediction for splicing factor 3B subunit 1 (O75533) · a predicted model of the same protein · chain C against A, TM-score 0.80
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q15393
- Every structure of UniProt Q9BWJ5
- Every structure of UniProt O75533
- Every structure of UniProt Q7RTV0
- Elsewhere: RCSB PDB 7B0I · PDBe 7B0I · UniProt Q15393 · UniProt Q9BWJ5 · UniProt O75533 · UniProt Q7RTV0
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