Research workbench
Crystal structure of box C/D RNP with 12 nt guide regions and 9 nt substrates
Analyse Crystal structure of box C/D RNP with 12 nt guide regions and 9 nt substrates in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GIN
- Type
- protein + RNA
- Length
- 2,297 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.308
- Source
- Sulfolobus solfataricus; SYNTHETIC CONSTRUCT
- Molecule
- C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; 50S ribosomal protein…
- EC
- 2.1.1.-
- UniProt
- A0A0E3MJI1, A0A0E3JZF7, A0A0E3JUC9
- Ligands
- SAH
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · resolution 3.308 · 7 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, K | C/D box methylation guide ribonucleoprotein complex aNOP56 subunit | protein | 375 | 65% helix, 6% strand | A0A0E3MJI1 |
| C, D, L | 50S ribosomal protein L7Ae | protein | 122 | 46% helix, 16% strand | A0A0E3JZF7 |
| E, F, M | Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase (EC 2.1.1.-) | protein | 227 | 26% helix, 30% strand | A0A0E3JUC9 |
| G | C/D RNA | rna | 35 | — | — |
| H | C/D RNA | rna | 32 | — | — |
| I, J, O | substrate | rna | 9 | — | — |
| N | C/D RNA | rna | 31 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains E, G, I, F, H, J, N, O, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.81 | 0.97 | 33 | SAH |
| 2 | 191 | 0.81 | 0.95 | 35 | SAH |
| 3 | 402 | 0.80 | 0.89 | 43 | empty |
| 4 | 158 | 0.80 | 0.96 | 30 | SAH |
| 5 | 406 | 0.77 | 0.87 | 54 | empty |
Interfaces
40 interfaces between chains.
- A–B · 1790 Ų buried · 13 hydrogen bonds · protein-protein
- K–M · 1498 Ų buried · 18 hydrogen bonds · protein-protein
- B–F · 1498 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 1487 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 1363 Ų buried · 113 hydrogen bonds · nucleic-nucleic
Compared structures
- 5GIN · Crystal structure of box C/D rnp with 12 nt guide regions and 9 nt substrates · 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 A0A0E3MJI1
- Every structure of UniProt A0A0E3JZF7
- Every structure of UniProt A0A0E3JUC9
- Elsewhere: RCSB PDB 5GIN · PDBe 5GIN · UniProt A0A0E3MJI1 · UniProt A0A0E3JZF7 · UniProt A0A0E3JUC9
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