Research workbench
Crystal structure of dmtailor in complex with cacagu RNA
Analyse Crystal structure of dmtailor in complex with cacagu RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I0V
- Type
- protein + RNA
- Length
- 350 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Terminal uridylyltransferase tailor; RNA (5'-R(*CP*AP*CP*AP*GP*U)-3')
- EC
- 2.7.7.52
- UniProt
- Q9VI58
- Ligands
- MG
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Terminal uridylyltransferase tailor (EC 2.7.7.52) | protein | 346 | 45% helix, 12% strand | Q9VI58 |
| B | RNA (5'-R(*CP*AP*CP*AP*GP*U)-3') | rna | 4 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
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 | 216 | 0.52 | 0.77 | 36 | empty |
| 2 | 76 | 0.40 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 670 Ų buried · 20 hydrogen bonds · protein-nucleic
Compared structures
- 6I0V · Crystal structure of DmTailor in complex with CACAGU RNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q9VI58 · AlphaFold monomer V2.0 prediction for terminal uridylyltransferase tailor (Q9VI58) · 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 Q9VI58
- Elsewhere: RCSB PDB 6I0V · PDBe 6I0V · UniProt Q9VI58
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