Research workbench
Structure of methylphosphate capping enzyme methyltransferase domain in complex with 5' end of 7SK RNA
Analyse Structure of methylphosphate capping enzyme methyltransferase domain in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DCC
- Type
- protein + RNA
- Length
- 257 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 7SK snrna methylphosphate capping enzyme; Human 7SK RNA stem-loop 1 proximal methylated
- EC
- 2.1.1.-
- UniProt
- Q7L2J0
- Ligands
- SAH, SO4
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 7SK snrna methylphosphate capping enzyme (EC 2.1.1.-) | protein | 221 | 40% helix, 20% strand | Q7L2J0 |
| B | Human 7SK RNA stem-loop 1 proximal methylated | rna | 36 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.77 | 0.97 | 31 | SAH |
| 2 | 126 | 0.40 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 936 Ų buried · 42 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6DCC · Structure of methylphosphate capping enzyme methyltransferase domain in complex with 5'… · the same entry in another collection · chain B against B, TM-score 1.00
- Q7L2J0 · AlphaFold monomer V2.0 prediction for 7SK snrna methylphosphate capping enzyme (Q7L2J0) · 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 Q7L2J0
- Elsewhere: RCSB PDB 6DCC · PDBe 6DCC · UniProt Q7L2J0
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