MolNFT v1 · #67195 · protein
Crystal structure of sulfolobus solfataricus NOP5 (1-262) and fibrillarin complex
3ID6 · Pre mRNA splicing protein: “Crystal structure of sulfolobus solfataricus NOP5 (1-262) and fibrillarin complex”. X-ray diffraction, 1 ligand (SAM), 2 pockets (best druggability 0.45). MolNFT v1 #67195 on GenesisL1: 3D structure…
- PDB
- 3ID6
- Type
- protein
- Length
- 478 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pre mRNA splicing protein; Fibrillarin-like RRNA/TRNA 2'-O-methyltransferase
- EC
- 2.1.1.-
- UniProt
- Q97ZH3, P58032
- Ligands
- SAM
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pre mRNA splicing protein | protein | 258 | 63% helix, 10% strand | Q97ZH3 |
| C | Fibrillarin-like RRNA/TRNA 2'-O-methyltransferase (EC 2.1.1.-) | protein | 220 | 24% helix, 33% strand | P58032 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.45 | 0.77 | 26 | SAM |
| 2 | 68 | 0.28 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–C · 1452 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3ID6 · Crystal structure of Sulfolobus solfataricus Nop5 (1-262) and fibrillarin complex · the same entry in another collection · chain A against A, TM-score 1.00
- P58032 · AlphaFold monomer V2.0 prediction for fibrillarin-like RRNA/TRNA 2'-O-methyltransferase… · a predicted model of the same protein · chain C against A, TM-score 0.96
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 Q97ZH3
- Every structure of UniProt P58032
- Elsewhere: RCSB PDB 3ID6 · PDBe 3ID6 · UniProt Q97ZH3 · UniProt P58032
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