Research workbench
Structure of mycobacterium hassiacum MET1 from orthorhombic crystals.
Analyse Structure of mycobacterium hassiacum MET1 from orthorhombic crystals. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G80
- Type
- protein
- Length
- 871 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyltransferase domain protein
- UniProt
- K5B7F3
- Ligands
- SAH
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyltransferase domain protein | protein | 213 | 40% helix, 24% strand | K5B7F3 |
| B | Methyltransferase domain protein | protein | 226 | 40% helix, 20% strand | K5B7F3 |
| M | Methyltransferase domain protein | protein | 218 | 39% helix, 21% strand | K5B7F3 |
| C | Methyltransferase domain protein | protein | 214 | 38% helix, 24% strand | K5B7F3 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains A, M, C
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.78 | 0.87 | 57 | SAH |
| 2 | 1111 | 0.77 | 0.79 | 128 | SAH |
| 3 | 362 | 0.66 | 0.80 | 32 | empty |
| 4 | 405 | 0.66 | 0.79 | 51 | empty |
| 5 | 229 | 0.55 | 0.78 | 38 | SAH |
Interfaces
5 interfaces between chains.
- A–B · 1499 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 471 Ų buried · 12 hydrogen bonds · protein-protein
- A–M · 425 Ų buried · 4 hydrogen bonds · protein-protein
- M–C · 402 Ų buried · 4 hydrogen bonds · protein-protein
- B–M · 214 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6G80 · Structure of Mycobacterium hassiacum MeT1 from orthorhombic crystals. · the same entry in another collection · chain C against C, TM-score 1.00
- K5B7F3 · AlphaFold monomer V2.0 prediction for mmp 1-O-methyltransferase (K5B7F3) · a predicted model of the same protein · chain M 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 K5B7F3
- Elsewhere: RCSB PDB 6G80 · PDBe 6G80 · UniProt K5B7F3
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