Research workbench
Crystal structure of mammalian capping enzyme (MCE1) and pol II ctd complex
Analyse Crystal structure of mammalian capping enzyme (MCE1) and pol II ctd complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RTX
- Type
- protein
- Length
- 529 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MRNA-capping enzyme; RNA polymerase II C-terminal domain
- EC
- 2.7.7.50
- UniProt
- O55236
- Ligands
- GUN
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MRNA-capping enzyme (EC 2.7.7.50) | protein | 262 | 28% helix, 31% strand | O55236 |
| B | MRNA-capping enzyme (EC 2.7.7.50) | protein | 254 | 27% helix, 31% strand | O55236 |
| C | RNA polymerase II C-terminal domain | protein | 13 | 0% helix, 0% strand | — |
Ligands and binding sites
- GUN · Guanine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 516 | 0.82 | 0.89 | 48 | empty |
| 2 | 1049 | 0.80 | 0.81 | 113 | empty |
| 3 | 328 | 0.68 | 0.82 | 44 | GUN |
| 4 | 357 | 0.68 | 0.81 | 48 | GUN |
| 5 | 81 | 0.52 | 0.84 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1100 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 395 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 390 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 3RTX · Crystal structure of mammalian capping enzyme (Mce1) and Pol II CTD complex · the same entry in another collection · chain A against A, TM-score 1.00
- O55236 · AlphaFold monomer V2.0 prediction for mRNA-capping enzyme (O55236) · 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 O55236
- Elsewhere: RCSB PDB 3RTX · PDBe 3RTX · UniProt O55236
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