Research workbench
Novel modifications on C-terminal domain of RNA polymerase II can fine- tune the phosphatase activity of SSU72.
Analyse Novel modifications on C-terminal domain of RNA polymerase II can fine- tune… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IMI
- Type
- protein
- Length
- 1,033 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Symplekin; CG14216; Ctd
- EC
- 3.1.3.16
- UniProt
- Q8MSU4, Q9VWE4
- Ligands
- PO4
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 68% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Symplekin | protein | 332 | 76% helix, 0% strand | Q8MSU4 |
| B, D | CG14216 (EC 3.1.3.16) | protein | 192 | 47% helix, 18% strand | Q9VWE4 |
| C | Symplekin | protein | 309 | 75% helix, 0% strand | Q8MSU4 |
| F | Ctd | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.75 | 0.89 | 38 | empty |
| 2 | 370 | 0.74 | 0.85 | 50 | empty |
| 3 | 689 | 0.73 | 0.79 | 65 | PO4 |
| 4 | 422 | 0.65 | 0.78 | 36 | empty |
| 5 | 331 | 0.63 | 0.80 | 34 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1314 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1308 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 853 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 654 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 4IMI · Novel Modifications on C-terminal Domain of RNA Polymerase II can Fine- tune the… · the same entry in another collection · chain B against B, TM-score 1.00
- Q8MSU4 · AlphaFold monomer V2.0 prediction for symplekin (Q8MSU4) · a predicted model of the same protein · chain C against A, TM-score 1.00
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 Q8MSU4
- Every structure of UniProt Q9VWE4
- Elsewhere: RCSB PDB 4IMI · PDBe 4IMI · UniProt Q8MSU4 · UniProt Q9VWE4
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