Research workbench
Structure of guanylylated mRNA capping enzyme complexed with GTP
Analyse Structure of guanylylated mRNA capping enzyme complexed with GTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CKN
- Type
- protein
- Length
- 634 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MRNA capping enzyme
- EC
- 2.7.7.50
- UniProt
- Q84424
- Ligands
- GTP, MN, SO4
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MRNA capping enzyme (EC 2.7.7.50) | protein | 317 | 21% helix, 40% strand | Q84424 |
| B | MRNA capping enzyme (EC 2.7.7.50) | protein | 317 | 21% helix, 42% strand | Q84424 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- MN · Manganese (II) ion · metal · chains B
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 718 | 0.81 | 0.85 | 97 | MN, SO4 |
| 2 | 241 | 0.69 | 0.85 | 43 | GTP |
| 3 | 252 | 0.62 | 0.81 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1694 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 1CKN · Structure of guanylylated mRNA capping enzyme complexed with GTP · the same entry in another collection · chain A 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 Q84424
- Elsewhere: RCSB PDB 1CKN · PDBe 1CKN · UniProt Q84424
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