MolNFT v1 · #174711 · protein + RNA
The crystal structure of trypanosoma brucei RNase D complex with RNA U12
7C45 · Cchc-type domain-containing protein: “The crystal structure of trypanosoma brucei RNase D complex with RNA U12”. X-ray diffraction, 2 ligands (ZN, CA), 3 pockets (best druggability 0.59). MolNFT v1 #174711 on GenesisL1: 3D…
- PDB
- 7C45
- Type
- protein + RNA
- Length
- 305 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cchc-type domain-containing protein; RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
- UniProt
- Q38DE2
- Ligands
- ZN, CA
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cchc-type domain-containing protein | protein | 295 | 46% helix, 12% strand | Q38DE2 |
| D | RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3') | rna | 10 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 348 | 0.59 | 0.77 | 48 | empty |
| 2 | 130 | 0.50 | 0.80 | 24 | empty |
| 3 | 75 | 0.36 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–D · 1239 Ų buried · 32 hydrogen bonds · protein-nucleic
Compared structures
- 7C45 · The crystal structure of Trypanosoma brucei RNase D complex with RNA U12 · 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 Q38DE2
- Elsewhere: RCSB PDB 7C45 · PDBe 7C45 · UniProt Q38DE2
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