MolNFT v1 · #185635 · protein + RNA
Substrate-bound a-like U2 snrnp
7Q4O · Splicing factor 3A subunit 2: “Substrate-bound a-like U2 snrnp”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.86). MolNFT v1 #185635 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7Q4O
- Type
- protein + RNA
- Length
- 2,564 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Splicing factor 3A subunit 2; U2 snrna; Splicing factor 3A subunit 3; Splicing factor 3B…
- UniProt
- Q15428, Q12874, O75533, Q13435, Q15393, Q9BWJ5, Q9Y3B4, Q7RTV0
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 10 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Splicing factor 3A subunit 2 | protein | 41 | 37% helix, 22% strand | Q15428 |
| 2 | U2 snrna | rna | 35 | — | — |
| 9 | Splicing factor 3A subunit 3 | protein | 98 | 47% helix, 8% strand | Q12874 |
| A | Splicing factor 3B subunit 1 | protein | 836 | 79% helix, 0% strand | O75533 |
| B | Splicing factor 3B subunit 2 | protein | 124 | 34% helix, 0% strand | Q13435 |
| C | Splicing factor 3B subunit 3 | protein | 1181 | 9% helix, 49% strand | Q15393 |
| E | Splicing factor 3B subunit 5 | protein | 65 | 62% helix, 0% strand | Q9BWJ5 |
| F | Splicing factor 3B subunit 6 | protein | 90 | 27% helix, 28% strand | Q9Y3B4 |
| G | Phd finger-like domain-containing protein 5A | protein | 81 | 19% helix, 25% strand | Q7RTV0 |
| h | Bps oligo | rna | 13 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains 1, 9, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.86 | 0.87 | 103 | empty |
| 2 | 1174 | 0.83 | 0.84 | 77 | empty |
| 3 | 319 | 0.80 | 0.91 | 53 | empty |
| 4 | 864 | 0.80 | 0.83 | 52 | empty |
| 5 | 967 | 0.77 | 0.79 | 92 | empty |
Interfaces
23 interfaces between chains.
- A–B · 2746 Ų buried · 23 hydrogen bonds · protein-protein
- C–E · 2274 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 1959 Ų buried · 25 hydrogen bonds · protein-protein
- A–F · 1661 Ų buried · 28 hydrogen bonds · protein-protein
- A–E · 1480 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 modified (nucleotide modification).
Compared structures
- 7Q4O · Substrate-bound A-like U2 snRNP · the same entry in another collection · chain h against h, 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 G against A, TM-score 0.99
- Q15393 · AlphaFold monomer V2.0 prediction for splicing factor 3B subunit 3 (Q15393) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q15428
- Every structure of UniProt Q12874
- Every structure of UniProt O75533
- Every structure of UniProt Q13435
- Every structure of UniProt Q15393
- Every structure of UniProt Q9BWJ5
- Every structure of UniProt Q9Y3B4
- Every structure of UniProt Q7RTV0
- Elsewhere: RCSB PDB 7Q4O · PDBe 7Q4O · UniProt Q15428 · UniProt Q12874 · UniProt O75533 · UniProt Q13435 · UniProt Q15393 · UniProt Q9BWJ5 · UniProt Q9Y3B4 · UniProt Q7RTV0
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