Research workbench
Crystal structure of bifunctional methyltransferase ycby (rlmlk) from escherichia COLI, SAM binding
Analyse Crystal structure of bifunctional methyltransferase ycby (rlmlk) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V8V
- Type
- protein
- Length
- 1,300 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal RNA large subunit methyltransferase L
- EC
- 2.1.1.173
- UniProt
- P75864
- Ligands
- SAM, TRV, GLC
- Pockets
- 19 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal RNA large subunit methyltransferase L (EC 2.1.1.173) | protein | 664 | 36% helix, 25% strand | P75864 |
| B | Ribosomal RNA large subunit methyltransferase L (EC 2.1.1.173) | protein | 636 | 36% helix, 24% strand | P75864 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 4 copies · chains A, B
- TRV · 6-O-octanoyl-beta-D-fructofuranose · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.73 | 0.77 | 91 | GLC, TRV, SAM |
| 2 | 466 | 0.71 | 0.81 | 56 | SAM |
| 3 | 799 | 0.71 | 0.77 | 61 | GLC, TRV |
| 4 | 451 | 0.69 | 0.80 | 55 | SAM |
| 5 | 71 | 0.50 | 0.83 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 959 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3V8V · Crystal structure of bifunctional methyltransferase YcbY (RlmLK) from Escherichia coli… · the same entry in another collection · chain B against B, TM-score 1.00
- P75864 · AlphaFold monomer V2.0 prediction for ribosomal RNA large subunit methyltransferase K/L… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P75864
- Elsewhere: RCSB PDB 3V8V · PDBe 3V8V · UniProt P75864
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