MolNFT v1 · #59013 · protein
Crystal structure of S-adenosylmethionine dependent methyltransferase (NP_104914.1) from mesorhizobium loti at 1.60 a resolution
3BKW: “Crystal structure of S-adenosylmethionine dependent methyltransferase (NP_104914.1) from mesorhizobium loti…”. X-ray diffraction, 3 pockets (best druggability 0.51). MolNFT v1 #59013 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3BKW
- Type
- protein
- Length
- 435 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine dependent methyltransferase
- UniProt
- Q98F67
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine dependent methyltransferase | protein | 219 | 34% helix, 28% strand | Q98F67 |
| B | S-adenosylmethionine dependent methyltransferase | protein | 216 | 33% helix, 28% strand | Q98F67 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 205 | 0.51 | 0.76 | 28 | empty |
| 2 | 185 | 0.48 | 0.76 | 30 | empty |
| 3 | 50 | 0.30 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1294 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3BKW · Crystal structure of S-adenosylmethionine dependent methyltransferase (NP_104914.1) from… · 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 Q98F67
- Elsewhere: RCSB PDB 3BKW · PDBe 3BKW · UniProt Q98F67
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