Research workbench
Crystal structure of sah-bound trmm from mycoplasma capricolum
Analyse Crystal structure of sah-bound trmm from mycoplasma capricolum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WM6
- Type
- protein
- Length
- 891 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyltransferase
- UniProt
- A0A0C2W699
- Ligands
- SAH, SO4
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyltransferase | protein | 240 | 31% helix, 30% strand | A0A0C2W699 |
| B | Methyltransferase | protein | 189 | 33% helix, 31% strand | A0A0C2W699 |
| C, D | Methyltransferase | protein | 231 | 30% helix, 32% strand | A0A0C2W699 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains A, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 949 | 0.82 | 0.83 | 96 | SAH |
| 2 | 162 | 0.77 | 0.93 | 33 | SAH |
| 3 | 175 | 0.76 | 0.92 | 38 | SAH |
| 4 | 148 | 0.40 | 0.73 | 27 | empty |
| 5 | 62 | 0.32 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1082 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1047 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 614 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7WM6 · Crystal structure of SAH-bound TrmM from Mycoplasma capricolum · 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 A0A0C2W699
- Elsewhere: RCSB PDB 7WM6 · PDBe 7WM6 · UniProt A0A0C2W699
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