Research workbench
The structure of the box CD enzyme reveals regulation of rRNA methylation
Analyse The structure of the box CD enzyme reveals regulation of rRNA methylation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BY9
- Type
- protein + RNA
- Length
- 3,044 residues
- Chains
- 18
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SSR26; NOP5/NOP56 related protein; 50S ribosomal protein L7AE; Fibrillarin-like RRNA/TRNA…
- EC
- 2.1.1.-
- UniProt
- Q8U4M1, Q8U160, Q8U4M2
- Pockets
- 20 · best druggability 0.89
Structure
solution nmr · 5 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | SSR26 | rna | 72 | — | — |
| C, F, I, L | NOP5/NOP56 related protein | protein | 366 | 62% helix, 6% strand | Q8U4M1 |
| D, G, J, M | 50S ribosomal protein L7AE | protein | 121 | 46% helix, 16% strand | Q8U160 |
| E, H, K, N | Fibrillarin-like RRNA/TRNA 2'-O-methyltransferase (EC 2.1.1.-) | protein | 227 | 26% helix, 31% strand | Q8U4M2 |
| W, X, Y, Z | 5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3' | rna | 11 | — | — |
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.89 | 0.91 | 111 | empty |
| 2 | 569 | 0.85 | 0.91 | 73 | empty |
| 3 | 1138 | 0.84 | 0.86 | 131 | empty |
| 4 | 303 | 0.78 | 0.90 | 36 | empty |
| 5 | 235 | 0.76 | 0.91 | 31 | empty |
Interfaces
50 interfaces between chains.
- I–L · 2103 Ų buried · 37 hydrogen bonds · protein-protein
- C–F · 2057 Ų buried · 29 hydrogen bonds · protein-protein
- A–F · 1623 Ų buried · 27 hydrogen bonds · protein-nucleic
- C–I · 1612 Ų buried · 34 hydrogen bonds · protein-protein
- A–I · 1464 Ų buried · 42 hydrogen bonds · protein-nucleic
Compared structures
- 4BY9 · The structure of the Box CD enzyme reveals regulation of rRNA methylation · the same entry in another collection · chain Z against Z, 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 Q8U4M1
- Every structure of UniProt Q8U160
- Every structure of UniProt Q8U4M2
- Elsewhere: RCSB PDB 4BY9 · PDBe 4BY9 · UniProt Q8U4M1 · UniProt Q8U160 · UniProt Q8U4M2
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