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Crystal structure of S-adenosylmethionine-dependent methyltransferase (NP_349143.1) from clostridium acetobutylicum at 2.00 a resolution
Analyse Crystal structure of S-adenosylmethionine-dependent methyltransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P8J
- Type
- protein
- Length
- 413 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine-dependent methyltransferase
- UniProt
- Q97G40
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine-dependent methyltransferase | protein | 206 | 26% helix, 36% strand | Q97G40 |
| B | S-adenosylmethionine-dependent methyltransferase | protein | 207 | 26% helix, 38% strand | Q97G40 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- PGE · Triethylene glycol · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 742 | 0.71 | 0.78 | 70 | SO4, GOL |
| 2 | 399 | 0.59 | 0.75 | 44 | SO4, GOL |
| 3 | 117 | 0.56 | 0.84 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1197 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified (engineered).
Compared structures
- 2P8J · Crystal structure of S-adenosylmethionine-dependent methyltransferase (NP_349143.1) 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 Q97G40
- Elsewhere: RCSB PDB 2P8J · PDBe 2P8J · UniProt Q97G40
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