Research workbench
Crystal structure of SAM-dependent methyltransferase (ZP_00538691.1) from exiguobacterium sp. 255-15 at 1.90 a resolution
Analyse Crystal structure of SAM-dependent methyltransferase (ZP_00538691.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D2L
- Type
- protein
- Length
- 956 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SAM-dependent methyltransferase
- UniProt
- Q41FK2
- Ligands
- MG
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | SAM-dependent methyltransferase | protein | 238 | 30% helix, 36% strand | Q41FK2 |
| C | SAM-dependent methyltransferase | protein | 242 | 31% helix, 33% strand | Q41FK2 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 595 | 0.75 | 0.81 | 59 | empty |
| 2 | 634 | 0.75 | 0.81 | 57 | empty |
| 3 | 606 | 0.74 | 0.80 | 60 | empty |
| 4 | 637 | 0.73 | 0.80 | 57 | empty |
| 5 | 184 | 0.50 | 0.77 | 23 | MG |
Interfaces
3 interfaces between chains.
- A–D · 391 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 286 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 20 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 3D2L · Crystal structure of SAM-dependent methyltransferase (ZP_00538691.1) from EXIGUOBACTERIUM… · 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 Q41FK2
- Elsewhere: RCSB PDB 3D2L · PDBe 3D2L · UniProt Q41FK2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.