Research workbench
Structure of the U2 5' module of the A3'-ssa complex
Analyse Structure of the U2 5' module of the A3'-ssa complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ONB
- Type
- protein + RNA
- Length
- 2,614 residues
- Chains
- 11
- Method
- electron microscopy
- 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
- Q15393, Q9BWJ5, O75533, Q7RTV0, Q13435, Q15428, Q12874, Q15427
- Ligands
- SJT, ZN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 11 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Splicing factor 3B subunit 3 | protein | 1190 | 8% helix, 43% strand | Q15393 |
| B | Splicing factor 3B subunit 5 | protein | 67 | 58% helix, 0% strand | Q9BWJ5 |
| C | Splicing factor 3B subunit 1 | protein | 816 | 80% helix, 0% strand | O75533 |
| D | Phd finger-like domain-containing protein 5A | protein | 81 | 14% helix, 26% strand | Q7RTV0 |
| F | Unk | protein | 21 | 71% helix, 0% strand | — |
| G | Minx | rna | 14 | — | — |
| H | RNU2 | rna | 32 | — | — |
| I | Splicing factor 3B subunit 2 | protein | 181 | 27% helix, 1% strand | Q13435 |
| M | Splicing factor 3A subunit 2 | protein | 47 | 40% helix, 19% strand | Q15428 |
| N | Splicing factor 3A subunit 3 | protein | 97 | 47% helix, 8% strand | Q12874 |
| K | Splicing factor 3B subunit 4 | protein | 68 | 29% helix, 34% strand | Q15427 |
Ligands and binding sites
- SJT · spliceostatin A (form II) · ligand · chains C, D
- ZN · Zinc ion · metal · 5 copies · chains D, M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 967 | 0.85 | 0.87 | 77 | empty |
| 2 | 1002 | 0.81 | 0.83 | 105 | empty |
| 3 | 773 | 0.81 | 0.84 | 95 | empty |
| 4 | 879 | 0.80 | 0.83 | 75 | empty |
| 5 | 584 | 0.79 | 0.85 | 86 | empty |
Interfaces
26 interfaces between chains.
- C–I · 2534 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 2364 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2356 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 1464 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1025 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7ONB · Structure of the U2 5' module of the A3'-SSA complex · the same entry in another collection · chain K against K, 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 0.98
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
- Every structure of UniProt Q13435
- Every structure of UniProt Q15428
- Every structure of UniProt Q12874
- Every structure of UniProt Q15427
- Elsewhere: RCSB PDB 7ONB · PDBe 7ONB · UniProt Q15393 · UniProt Q9BWJ5 · UniProt O75533 · UniProt Q7RTV0 · UniProt Q13435 · UniProt Q15428 · UniProt Q12874 · UniProt Q15427
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