MolNFT v1 · #73222 · protein
Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle
3NVM · NOP5/NOP56 related protein: “Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle”. X-ray diffraction, 4 pockets (best druggability 0.67). MolNFT v1 #73222 on GenesisL1: 3D structure, binding…
- PDB
- 3NVM
- Type
- protein
- Length
- 569 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NOP5/NOP56 related protein; Fibrillarin-like RRNA/TRNA 2'-O-methyltransferase
- EC
- 2.1.1.-
- UniProt
- Q8U4M1, Q8U4M2
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NOP5/NOP56 related protein | protein | 342 | 59% helix, 5% strand | Q8U4M1 |
| B | Fibrillarin-like RRNA/TRNA 2'-O-methyltransferase (EC 2.1.1.-) | protein | 227 | 23% helix, 26% strand | Q8U4M2 |
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.67 | 0.94 | 23 | empty |
| 2 | 234 | 0.57 | 0.78 | 28 | empty |
| 3 | 257 | 0.55 | 0.77 | 32 | empty |
| 4 | 55 | 0.32 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 2035 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3NVM · Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle · the same entry in another collection · chain A against A, 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 B against A, TM-score 0.98
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 Q8U4M2
- Elsewhere: RCSB PDB 3NVM · PDBe 3NVM · UniProt Q8U4M1 · UniProt Q8U4M2
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