MolNFT v1 · #185615 · protein + RNA
Human 17S U2 snrnp 5' domain
7Q3L · Splicing factor 3B subunit 2: “Human 17S U2 snrnp 5' domain”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.85). MolNFT v1 #185615 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7Q3L
- Type
- protein + RNA
- Length
- 2,481 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Splicing factor 3B subunit 2; Splicing factor 3B subunit 3; Splicing factor 3B subunit 5…
- EC
- 3.6.4.13
- UniProt
- Q13435, Q15393, Q9BWJ5, Q7RTV0, Q12874, O43719, O75533, Q7L014
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 9 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Splicing factor 3B subunit 2 | protein | 110 | 39% helix, 0% strand | Q13435 |
| C | Splicing factor 3B subunit 3 | protein | 1189 | 9% helix, 48% strand | Q15393 |
| E | Splicing factor 3B subunit 5 | protein | 70 | 64% helix, 0% strand | Q9BWJ5 |
| G | Phd finger-like domain-containing protein 5A | protein | 81 | 17% helix, 22% strand | Q7RTV0 |
| 2 | U2 snrna | rna | 41 | — | — |
| 9 | Splicing factor 3A subunit 3 | protein | 92 | 47% helix, 7% strand | Q12874 |
| q | HIV tat-specific factor 1 | protein | 66 | 33% helix, 20% strand | O43719 |
| A | Splicing factor 3B subunit 1 | protein | 814 | 80% helix, 0% strand | O75533 |
| p | Probable ATP-dependent RNA helicase DDX46 (EC 3.6.4.13) | protein | 18 | 83% helix, 0% strand | Q7L014 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains G, 9
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.85 | 0.86 | 111 | empty |
| 2 | 1067 | 0.83 | 0.84 | 76 | empty |
| 3 | 892 | 0.81 | 0.83 | 97 | empty |
| 4 | 958 | 0.80 | 0.82 | 84 | empty |
| 5 | 818 | 0.80 | 0.83 | 55 | empty |
Interfaces
17 interfaces between chains.
- B–A · 2405 Ų buried · 26 hydrogen bonds · protein-protein
- C–E · 2352 Ų buried · 37 hydrogen bonds · protein-protein
- C–A · 2337 Ų buried · 29 hydrogen bonds · protein-protein
- E–A · 1671 Ų buried · 33 hydrogen bonds · protein-protein
- q–A · 1191 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 7Q3L · Human 17S U2 snRNP 5' domain · the same entry in another collection · chain p against p, 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 C against A, TM-score 0.99
- 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 0.98
- O43719 · AlphaFold monomer V2.0 prediction for HIV tat-specific factor 1 (O43719) · a predicted model of the same protein · chain q against A, TM-score 0.94
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 Q13435
- Every structure of UniProt Q15393
- Every structure of UniProt Q9BWJ5
- Every structure of UniProt Q7RTV0
- Every structure of UniProt Q12874
- Every structure of UniProt O43719
- Every structure of UniProt O75533
- Every structure of UniProt Q7L014
- Elsewhere: RCSB PDB 7Q3L · PDBe 7Q3L · UniProt Q13435 · UniProt Q15393 · UniProt Q9BWJ5 · UniProt Q7RTV0 · UniProt Q12874 · UniProt O43719 · UniProt O75533 · UniProt Q7L014
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