MolNFT v1 · #119891 · protein + RNA
Crystal structure of box C/D rnp with 12 nt guide regions and 13 nt substrates
5GIO · C/D box methylation guide ribonucleoprotein complex ANOP56…: “Crystal structure of box C/D rnp with 12 nt guide regions and 13 nt substrates”. X-ray diffraction, 1 ligand (SAH), 20 pockets (best druggability 0.85). MolNFT v1 #119891…
- PDB
- 5GIO
- Type
- protein + RNA
- Length
- 2,300 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 0.85
Structure
x-ray diffraction · 7 distinct chains · 50% helix, 16% 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, 7% strand | A0A0E3MJI1 |
| C, D, L | 50S ribosomal protein L7AE | protein | 122 | 47% helix, 16% strand | A0A0E3JZF7 |
| E, F, M | Fibrillarin-like RRNA/TRNA 2'-O-methyltransferase (EC 2.1.1.-) | protein | 227 | 28% helix, 32% strand | A0A0E3JUC9 |
| G | C/D RNA | rna | 35 | — | — |
| H | C/D RNA | rna | 32 | — | — |
| I, J, O | Substrate | rna | 10 | — | — |
| 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.85 | 0.86 | 71 | empty |
| 2 | 987 | 0.80 | 0.82 | 84 | empty |
| 3 | 171 | 0.80 | 0.96 | 30 | SAH |
| 4 | 152 | 0.80 | 0.97 | 30 | SAH |
| 5 | 151 | 0.80 | 0.97 | 31 | SAH |
Interfaces
40 interfaces between chains.
- A–B · 1814 Ų buried · 16 hydrogen bonds · protein-protein
- K–M · 1494 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 1485 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 1479 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 1343 Ų buried · 112 hydrogen bonds · nucleic-nucleic
Compared structures
- 5GIO · Crystal structure of box C/D RNP with 12 nt guide regions and 13 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 5GIO · PDBe 5GIO · UniProt A0A0E3MJI1 · UniProt A0A0E3JZF7 · UniProt A0A0E3JUC9
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