MolNFT v1 · #146264 · protein + RNA
Structure of methylphosphate capping enzyme methyltransferase domain in complex with 5' end of 7SK RNA
6DCC · 7SK snrna methylphosphate capping enzyme: “Structure of methylphosphate capping enzyme methyltransferase domain in complex with 5' end of 7SK RNA”. X-ray diffraction, 2 ligands (SAH, SO4), 2 pockets (best druggability 0.77). MolNFT…
- 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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