MolNFT v1 · #88194 · protein
Crystal structure of sulfolobus acidocaldarius trmj in complex with S-adenosyl-L-homocysteine
4CNG · Spou rRNA methylase: “Crystal structure of sulfolobus acidocaldarius trmj in complex with S-adenosyl-L-homocysteine”. X-ray diffraction, 1 ligand (SAH), 3 pockets (best druggability 0.65). MolNFT v1 #88194 on GenesisL1: 3D…
- PDB
- 4CNG
- Type
- protein
- Length
- 304 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spou rRNA methylase
- EC
- 2.1.1.200
- UniProt
- Q4JB16
- Ligands
- SAH
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spou rRNA methylase (EC 2.1.1.200) | protein | 156 | 42% helix, 21% strand | Q4JB16 |
| B | Spou rRNA methylase (EC 2.1.1.200) | protein | 148 | 40% helix, 22% strand | Q4JB16 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.65 | 0.84 | 33 | SAH |
| 2 | 175 | 0.60 | 0.82 | 30 | SAH |
| 3 | 54 | 0.33 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1424 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 4CNG · Crystal structure of Sulfolobus acidocaldarius TrmJ in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q4JB16 · AlphaFold monomer V2.0 prediction for tRNA (cytidine-2'-O-)-methyltransferase trmj… · 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 Q4JB16
- Elsewhere: RCSB PDB 4CNG · PDBe 4CNG · UniProt Q4JB16
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