Research workbench
Semet-derivative of a methyltransferase from M. mazei
Analyse Semet-derivative of a methyltransferase from M. mazei in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AY8
- Type
- protein
- Length
- 680 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylcobalamin\: coenzyme M methyltransferase
- EC
- 2.1.1.247
- UniProt
- Q8PXZ6
- Ligands
- COM, ZN
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Methylcobalamin\: coenzyme M methyltransferase (EC 2.1.1.247) | protein | 340 | 51% helix, 12% strand | Q8PXZ6 |
Ligands and binding sites
- COM · 1-thioethanesulfonic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.61 | 0.81 | 29 | empty |
| 2 | 189 | 0.49 | 0.76 | 31 | COM |
| 3 | 214 | 0.49 | 0.75 | 34 | COM |
| 4 | 67 | 0.33 | 0.76 | 14 | empty |
| 5 | 75 | 0.29 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 563 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered, oxidation).
Compared structures
- 4AY8 · SeMet-derivative of a methyltransferase from M. mazei · 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 Q8PXZ6
- Elsewhere: RCSB PDB 4AY8 · PDBe 4AY8 · UniProt Q8PXZ6
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