MolNFT v1 · #121454 · protein
Crystal structure of escherichia COLI 16S rRNA methyltransferase rsmi in complex with adomet
5HW4 · Ribosomal RNA small subunit methyltransferase I: “Crystal structure of escherichia COLI 16S rRNA methyltransferase rsmi in complex with adomet”. X-ray diffraction, 1 ligand (SAM), 6 pockets (best druggability 0.61). MolNFT v1…
- PDB
- 5HW4
- Type
- protein
- Length
- 672 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal RNA small subunit methyltransferase I
- EC
- 2.1.1.198
- UniProt
- P67087
- Ligands
- SAM
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal RNA small subunit methyltransferase I (EC 2.1.1.198) | protein | 228 | 38% helix, 21% strand | P67087 |
| B | Ribosomal RNA small subunit methyltransferase I (EC 2.1.1.198) | protein | 222 | 38% helix, 22% strand | P67087 |
| C | Ribosomal RNA small subunit methyltransferase I (EC 2.1.1.198) | protein | 222 | 39% helix, 22% strand | P67087 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.61 | 0.83 | 25 | SAM |
| 2 | 187 | 0.61 | 0.82 | 25 | SAM |
| 3 | 170 | 0.59 | 0.82 | 26 | SAM |
| 4 | 365 | 0.58 | 0.76 | 44 | empty |
| 5 | 51 | 0.31 | 0.76 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2226 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 472 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5HW4 · Crystal structure of Escherichia coli 16S rRNA methyltransferase RsmI in complex with… · the same entry in another collection · chain B against B, TM-score 1.00
- P67087 · AlphaFold monomer V2.0 prediction for ribosomal RNA small subunit methyltransferase I… · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P67087
- Elsewhere: RCSB PDB 5HW4 · PDBe 5HW4 · UniProt P67087
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