MolNFT v1 · #61031 · protein
Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the carboxy-terminal domain of RNA-polymerase II
3D9L · 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 (BTN), 1 pocket (best druggability 0.51). MolNFT v1 #61031 on…
- PDB
- 3D9L
- Type
- protein
- Length
- 297 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
- BTN
- Pockets
- 1 · best druggability 0.51
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 | 140 | 81% helix, 0% strand | Q9UPN6 |
| B | RNA-binding protein 16 | protein | 139 | 81% helix, 1% strand | Q9UPN6 |
| Y | Ctd-peptide | protein | 10 | 0% helix, 0% strand | — |
| Z | Ctd-peptide | protein | 8 | 0% helix, 13% strand | — |
Ligands and binding sites
- BTN · Biotin · ligand · chains A, B, Y
- ACT · Acetate ion · additive · chains A, Y
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.51 | 0.79 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–Y · 675 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 494 Ų buried · 10 hydrogen bonds · protein-protein
- B–Z · 466 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified, 1 cofactor (phosphorylation, biotinylation).
Compared structures
- 3D9L · 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 B 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 3D9L · PDBe 3D9L · UniProt Q9UPN6
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