Research workbench
Crystal structure of escherichia COLI 16S rRNA methyltransferase rsmi in complex with adomet
Analyse Crystal structure of escherichia COLI 16S rRNA methyltransferase rsmi in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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