Research workbench
Structure of a minimal SF3B core in complex with the inactive modulator spliceostatin E (form I)
Analyse Structure of a minimal SF3B core in complex with the inactive modulator… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OPI
- Type
- protein
- Length
- 1,863 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Splicing factor 3B subunit 3; Splicing factor 3B subunit 5; Splicing factor 3B subunit 1…
- UniProt
- Q921M3, Q15393, Q9BWJ5, O75533, Q7RTV0
- Ligands
- 07I, ZN
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Splicing factor 3B subunit 3 | protein | 863 | 11% helix, 45% strand | Q921M3, Q15393 |
| B | Splicing factor 3B subunit 5 | protein | 65 | 60% helix, 0% strand | Q9BWJ5 |
| C | Splicing factor 3B subunit 1 | protein | 842 | 77% helix, 0% strand | O75533 |
| D | Phd finger-like domain-containing protein 5A | protein | 93 | 12% helix, 29% strand | Q7RTV0 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1062 | 0.85 | 0.86 | 75 | empty |
| 2 | 940 | 0.79 | 0.81 | 109 | empty |
| 3 | 1165 | 0.77 | 0.79 | 101 | empty |
| 4 | 98 | 0.76 | 0.97 | 22 | empty |
| 5 | 932 | 0.75 | 0.78 | 75 | 07I |
Interfaces
5 interfaces between chains.
- A–B · 2362 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 2245 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1498 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1259 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 595 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7OPI · Structure of a minimal SF3B core in complex with the inactive modulator spliceostatin E… · the same entry in another collection · chain A against A, 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
- Q921M3 · AlphaFold monomer V2.0 prediction for splicing factor 3B subunit 3 (Q921M3) · 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 0.89
- 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 0.81
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 Q921M3
- Every structure of UniProt Q15393
- Every structure of UniProt Q9BWJ5
- Every structure of UniProt O75533
- Every structure of UniProt Q7RTV0
- Elsewhere: RCSB PDB 7OPI · PDBe 7OPI · UniProt Q921M3 · UniProt Q15393 · UniProt Q9BWJ5 · UniProt O75533 · UniProt Q7RTV0
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