Research workbench
Crystal structure of the SAM dependent methyltransferase from agrobacterium tumefaciens
Analyse Crystal structure of the SAM dependent methyltransferase from agrobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IGT
- Type
- protein
- Length
- 938 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SAM dependent methyltransferase
- UniProt
- Q8UIF7
- Ligands
- SAM
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SAM dependent methyltransferase | protein | 313 | 25% helix, 33% strand | Q8UIF7 |
| B | SAM dependent methyltransferase | protein | 312 | 25% helix, 34% strand | Q8UIF7 |
| C | SAM dependent methyltransferase | protein | 313 | 25% helix, 33% strand | Q8UIF7 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 3 copies · chains A, C, B
- FMT · Formic acid · additive · 7 copies · chains A, B, C
- ACY · Acetic acid · additive · 6 copies · chains A, C
- GOL · Glycerol · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.77 | 0.97 | 22 | empty |
| 2 | 106 | 0.75 | 0.96 | 22 | empty |
| 3 | 102 | 0.75 | 0.96 | 23 | empty |
| 4 | 531 | 0.68 | 0.78 | 54 | SAM, FMT |
| 5 | 495 | 0.68 | 0.79 | 56 | SAM, FMT |
Interfaces
3 interfaces between chains.
- B–C · 777 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 766 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 679 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 2IGT · Crystal Structure of the SAM Dependent Methyltransferase from Agrobacterium tumefaciens · the same entry in another collection · chain C against C, 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 Q8UIF7
- Elsewhere: RCSB PDB 2IGT · PDBe 2IGT · UniProt Q8UIF7
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