MolNFT v1 · #114650 · protein
Crystal structure of the 16S rRNA (ADENINE(1408)-N(1))- methyltransferase W203A mutant with cosubstrate SAM from catenulisporales acidiphilia
5BW4 · 16S rRNA (ADENINE(1408)-N(1))-methyltransferase: “Crystal structure of the 16S rRNA (ADENINE(1408)-N(1))- methyltransferase W203A mutant with cosubstrate SAM…”. X-ray diffraction, 1 ligand (SAM), 6 pockets (best druggability 0.62).…
- PDB
- 5BW4
- Type
- protein
- Length
- 429 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S rRNA (ADENINE(1408)-N(1))-methyltransferase
- UniProt
- C7Q5P8
- Ligands
- SAM
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S rRNA (ADENINE(1408)-N(1))-methyltransferase | protein | 205 | 38% helix, 29% strand | C7Q5P8 |
| B | 16S rRNA (ADENINE(1408)-N(1))-methyltransferase | protein | 224 | 33% helix, 28% strand | C7Q5P8 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.62 | 0.91 | 22 | empty |
| 2 | 148 | 0.60 | 0.84 | 31 | SAM |
| 3 | 123 | 0.45 | 0.78 | 24 | SAM |
| 4 | 98 | 0.41 | 0.77 | 23 | empty |
| 5 | 114 | 0.40 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 766 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5BW4 · Crystal structure of the 16S rRNA (adenine(1408)-N(1))-methyltransferase W203A mutant… · the same entry in another collection · chain A against A, TM-score 1.00
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 C7Q5P8
- Elsewhere: RCSB PDB 5BW4 · PDBe 5BW4 · UniProt C7Q5P8
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