MolNFT v1 · #122108 · protein
Crystal structure of the human SF3B core complex
5IFE · Splicing factor 3B subunit 5: “Crystal structure of the human SF3B core complex”. X-ray diffraction, 2 ligands (ZN, K), 20 pockets (best druggability 0.84). MolNFT v1 #122108 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5IFE
- Type
- protein
- Length
- 2,168 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Splicing factor 3B subunit 5; Splicing factor 3B subunit 1; Phd finger-like…
- UniProt
- Q9BWJ5, O75533, Q7RTV0, Q15393
- Ligands
- ZN, K
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Splicing factor 3B subunit 5 | protein | 66 | 58% helix, 0% strand | Q9BWJ5 |
| C | Splicing factor 3B subunit 1 | protein | 829 | 76% helix, 0% strand | O75533 |
| D | Phd finger-like domain-containing protein 5A | protein | 89 | 12% helix, 27% strand | Q7RTV0 |
| A | Splicing factor 3B subunit 3 | protein | 1184 | 7% helix, 48% strand | Q15393 |
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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.84 | 0.85 | 79 | empty |
| 2 | 1163 | 0.80 | 0.81 | 127 | empty |
| 3 | 868 | 0.80 | 0.82 | 64 | empty |
| 4 | 324 | 0.79 | 0.90 | 45 | empty |
| 5 | 1144 | 0.77 | 0.79 | 98 | empty |
Interfaces
5 interfaces between chains.
- C–A · 2338 Ų buried · 19 hydrogen bonds · protein-protein
- B–A · 2320 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1588 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1254 Ų buried · 9 hydrogen bonds · protein-protein
- D–A · 589 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5IFE · Crystal structure of the human SF3b core complex · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.92
- 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 0.91
- 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 0.83
- 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 Q9BWJ5
- Every structure of UniProt O75533
- Every structure of UniProt Q7RTV0
- Every structure of UniProt Q15393
- Elsewhere: RCSB PDB 5IFE · PDBe 5IFE · UniProt Q9BWJ5 · UniProt O75533 · UniProt Q7RTV0 · UniProt Q15393
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