Research workbench
Crystal structure of antibiotic related methyltransferase
Analyse Crystal structure of antibiotic related methyltransferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LCV
- Type
- protein
- Length
- 259 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sisomicin-gentamicin resistance methylase sgm
- UniProt
- Q7M0R2
- Ligands
- SAM
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Sisomicin-gentamicin resistance methylase sgm | protein | 259 | 51% helix, 15% strand | Q7M0R2 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.74 | 0.90 | 39 | SAM |
| 2 | 65 | 0.41 | 0.81 | 17 | empty |
| 3 | 56 | 0.30 | 0.75 | 12 | empty |
| 4 | 53 | 0.28 | 0.74 | 15 | empty |
Modifications
Observed in the structure: 3 modified (engineered).
Compared structures
- 3LCV · Crystal Structure of Antibiotic related Methyltransferase · the same entry in another collection · chain B against B, TM-score 1.00
- Q7M0R2 · AlphaFold monomer V2.0 prediction for 16S rRNA (GUANINE(1405)-N(7))-methyltransferase… · 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 Q7M0R2
- Elsewhere: RCSB PDB 3LCV · PDBe 3LCV · UniProt Q7M0R2
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