Research workbench
Crystal structure of substrate-bound halfmer box C/D rnp
Analyse Crystal structure of substrate-bound halfmer box C/D rnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NMU
- Type
- protein + RNA
- Length
- 1,521 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NOP5/NOP56 related protein; 50S ribosomal protein L7AE; RNA (34-mer); Fibrillarin-like…
- EC
- 2.1.1.-
- UniProt
- Q8U4M1, Q8U160, Q8U4M2
- Ligands
- SAM
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NOP5/NOP56 related protein | protein | 366 | 64% helix, 6% strand | Q8U4M1 |
| C, G | 50S ribosomal protein L7AE | protein | 121 | 42% helix, 17% strand | Q8U160 |
| D, E | RNA (34-mer) | rna | 34 | — | — |
| F, J | Fibrillarin-like RRNA/TRNA 2'-O-methyltransferase (EC 2.1.1.-) | protein | 227 | 26% helix, 31% strand | Q8U4M2 |
| I | RNA (5'-R(*GP*AP*GP*CP*UP*UP*CP*AP*AP*CP*GP*GP*C)-3') | rna | 13 | — | — |
| K | RNA (5'-R(*GP*AP*GP*CP*UP*UP*CP*AP*AP*CP*GP*GP*C)-3') | rna | 12 | — | — |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, F, B, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1113 | 0.80 | 0.82 | 90 | SAM |
| 2 | 990 | 0.80 | 0.81 | 89 | SAM |
| 3 | 437 | 0.63 | 0.78 | 46 | empty |
| 4 | 525 | 0.60 | 0.74 | 37 | empty |
| 5 | 273 | 0.60 | 0.79 | 28 | empty |
Interfaces
18 interfaces between chains.
- A–B · 1930 Ų buried · 19 hydrogen bonds · protein-protein
- A–F · 1915 Ų buried · 17 hydrogen bonds · protein-protein
- B–J · 1891 Ų buried · 22 hydrogen bonds · protein-protein
- B–E · 1279 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–D · 1183 Ų buried · 26 hydrogen bonds · protein-nucleic
Compared structures
- 3NMU · Crystal Structure of substrate-bound halfmer box C/D RNP · the same entry in another collection · chain K against K, TM-score 1.00
- Q8U4M2 · AlphaFold monomer V2.0 prediction for fibrillarin-like RRNA/TRNA 2'-O-methyltransferase… · a predicted model of the same protein · chain F 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 Q8U4M1
- Every structure of UniProt Q8U160
- Every structure of UniProt Q8U4M2
- Elsewhere: RCSB PDB 3NMU · PDBe 3NMU · UniProt Q8U4M1 · UniProt Q8U160 · UniProt Q8U4M2
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