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Structure of an mRNA capping enzyme bound to the phosphorylated carboxyl-terminal domain of RNA polymerase II
Analyse Structure of an mRNA capping enzyme bound to the phosphorylated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1P16
- Type
- protein
- Length
- 793 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MRNA capping enzyme alpha subunit; Phosphorylated peptide from C-terminal of RNA…
- EC
- 2.7.7.50
- UniProt
- P78587
- Ligands
- G, GTP, PO4
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MRNA capping enzyme alpha subunit (EC 2.7.7.50) | protein | 390 | 28% helix, 33% strand | P78587 |
| B | MRNA capping enzyme alpha subunit (EC 2.7.7.50) | protein | 377 | 28% helix, 30% strand | P78587 |
| C | Phosphorylated peptide from C-terminal of RNA polymerase II | protein | 9 | 0% helix, 0% strand | — |
| D | Phosphorylated peptide from C-terminal of RNA polymerase II | protein | 17 | 0% helix, 0% strand | — |
Ligands and binding sites
- G · Guanosine-5'-monophosphate · ligand · chains A
- GTP · Guanosine-5'-triphosphate · ligand · chains B
- PO4 · Phosphate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 980 | 0.82 | 0.83 | 67 | empty |
| 2 | 205 | 0.66 | 0.84 | 33 | GTP |
| 3 | 236 | 0.63 | 0.82 | 37 | PO4, G |
| 4 | 364 | 0.56 | 0.75 | 45 | empty |
| 5 | 275 | 0.51 | 0.74 | 39 | empty |
Interfaces
6 interfaces between chains.
- B–D · 785 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 453 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 207 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 158 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 97 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 modified, 1 covalent (engineered, phosphorylation, covalent ligand).
Compared structures
- 1P16 · Structure of an mRNA capping enzyme bound to the phosphorylated carboxyl-terminal domain… · the same entry in another collection · chain A against A, TM-score 1.00
- P78587 · AlphaFold monomer V2.0 prediction for mRNA-capping enzyme subunit alpha (P78587) · 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 P78587
- Elsewhere: RCSB PDB 1P16 · PDBe 1P16 · UniProt P78587
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