MolNFT v1 · #61033 · protein
Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the carboxy-terminal domain of RNA-polymerase II
3D9N · RNA-binding protein 16: “Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the carboxy-terminal…”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.49). MolNFT v1 #61033 on…
- PDB
- 3D9N
- Type
- protein
- Length
- 294 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-binding protein 16; Ctd-peptide
- UniProt
- Q9UPN6
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.49
Structure
x-ray diffraction · 3 distinct chains · 79% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-binding protein 16 | protein | 138 | 81% helix, 1% strand | Q9UPN6 |
| B | RNA-binding protein 16 | protein | 140 | 81% helix, 1% strand | Q9UPN6 |
| Y, Z | Ctd-peptide | protein | 8 | 0% helix, 13% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, Y, B, Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.49 | 0.78 | 16 | empty |
| 2 | 68 | 0.42 | 0.80 | 17 | empty |
| 3 | 56 | 0.37 | 0.80 | 13 | empty |
| 4 | 54 | 0.33 | 0.78 | 17 | SO4 |
| 5 | 53 | 0.31 | 0.77 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–Y · 501 Ų buried · 8 hydrogen bonds · protein-protein
- B–Z · 500 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 446 Ų buried · 10 hydrogen bonds · protein-protein
- B–Y · 84 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 3D9N · Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UPN6 · AlphaFold monomer V2.0 prediction for sr-related and ctd-associated factor 8 (Q9UPN6) · a predicted model of the same protein · chain A 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 Q9UPN6
- Elsewhere: RCSB PDB 3D9N · PDBe 3D9N · UniProt Q9UPN6
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