MolNFT v1 · #77943 · protein
Crystal structure of mammalian capping enzyme (MCE1) and pol II ctd complex
3RTX · MRNA-capping enzyme: “Crystal structure of mammalian capping enzyme (MCE1) and pol II ctd complex”. X-ray diffraction, 1 ligand (GUN), 6 pockets (best druggability 0.82). MolNFT v1 #77943 on GenesisL1: 3D structure, binding sites…
- 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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