Research workbench
Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the carboxy-terminal domain of RNA-polymerase II
Analyse Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D9K
- Type
- protein
- Length
- 293 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
- 3 · best druggability 0.44
Structure
x-ray diffraction · 4 distinct chains · 76% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-binding protein 16 | protein | 137 | 81% helix, 1% strand | Q9UPN6 |
| B | RNA-binding protein 16 | protein | 141 | 80% helix, 0% strand | Q9UPN6 |
| Y | Ctd-peptide | protein | 6 | 0% helix, 17% strand | — |
| Z | Ctd-peptide | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.44 | 0.78 | 22 | empty |
| 2 | 57 | 0.35 | 0.78 | 16 | empty |
| 3 | 53 | 0.28 | 0.75 | 14 | empty |
Interfaces
4 interfaces between chains.
- B–Z · 668 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 479 Ų buried · 9 hydrogen bonds · protein-protein
- A–Y · 362 Ų buried · 3 hydrogen bonds · protein-protein
- B–Y · 93 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 3D9K · 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 3D9K · PDBe 3D9K · UniProt Q9UPN6
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