MolNFT v1 · #88193 · protein
Crystal structure of sulfolobus acidocaldarius trmj
4CNF · Spou rRNA methylase: “Crystal structure of sulfolobus acidocaldarius trmj”. X-ray diffraction, 1 ligand (MTA), 3 pockets (best druggability 0.65). MolNFT v1 #88193 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4CNF
- Type
- protein
- Length
- 306 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
- MTA
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spou rRNA methylase (EC 2.1.1.200) | protein | 155 | 36% helix, 21% strand | Q4JB16 |
| B | Spou rRNA methylase (EC 2.1.1.200) | protein | 151 | 39% helix, 20% strand | Q4JB16 |
Ligands and binding sites
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
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 | 246 | 0.65 | 0.82 | 37 | empty |
| 2 | 179 | 0.61 | 0.83 | 28 | PEG, MTA |
| 3 | 70 | 0.34 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1542 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
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 4CNF · PDBe 4CNF · UniProt Q4JB16
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