MolNFT v1 · #134781 · protein + RNA
Structure and conformational plasticity of the U6 small nuclear ribonucleoprotein core
5TF6 · U4/U6 snrna-associated-splicing factor PRP24: “Structure and conformational plasticity of the U6 small nuclear ribonucleoprotein core”. X-ray diffraction, 2 ligands (K, CL), 14 pockets (best druggability 0.75). MolNFT v1 #134781 on…
- PDB
- 5TF6
- Type
- protein + RNA
- Length
- 856 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U4/U6 snrna-associated-splicing factor PRP24; U6 snrna
- UniProt
- P49960
- Ligands
- K, CL
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | U4/U6 snrna-associated-splicing factor PRP24 | protein | 367 | 35% helix, 29% strand | P49960 |
| B | U6 snrna | rna | 71 | — | — |
| C | U4/U6 snrna-associated-splicing factor PRP24 | protein | 366 | 33% helix, 29% strand | P49960 |
| D | U6 snrna | rna | 52 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · 5 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, C, B, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.75 | 0.97 | 22 | CL, GOL |
| 2 | 265 | 0.67 | 0.84 | 34 | empty |
| 3 | 306 | 0.66 | 0.82 | 34 | empty |
| 4 | 178 | 0.65 | 0.85 | 40 | empty |
| 5 | 150 | 0.59 | 0.83 | 28 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2739 Ų buried · 77 hydrogen bonds · protein-nucleic
- C–D · 2719 Ų buried · 72 hydrogen bonds · protein-nucleic
- A–C · 657 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 225 Ų buried · 3 hydrogen bonds · protein-nucleic
- A–D · 65 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 5TF6 · Structure and conformational plasticity of the U6 small nuclear ribonucleoprotein core · the same entry in another collection · chain A against A, TM-score 1.00
- P49960 · AlphaFold monomer V2.0 prediction for U4/U6 snrna-associated-splicing factor PRP24… · a predicted model of the same protein · chain A 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 P49960
- Elsewhere: RCSB PDB 5TF6 · PDBe 5TF6 · UniProt P49960
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