MolNFT v1 · #168857 · protein
Structure of radical S-adenosylmethionine methyltransferase, tsrm, from kitasatospora setae with cobalamin and [4FE-4S] cluster bound
6WTE · B12-binding domain-containing protein: “Structure of radical S-adenosylmethionine methyltransferase, tsrm, from kitasatospora setae with cobalamin…”. X-ray diffraction, 2 ligands (SF4, B12), 12 pockets (best druggability 0.85).…
- PDB
- 6WTE
- Type
- protein
- Length
- 1,097 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- B12-binding domain-containing protein
- UniProt
- E4N8S5
- Ligands
- SF4, B12
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | B12-binding domain-containing protein | protein | 567 | 38% helix, 16% strand | E4N8S5 |
| B | B12-binding domain-containing protein | protein | 530 | 40% helix, 16% strand | E4N8S5 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- B12 · Cobalamin · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1098 | 0.85 | 0.86 | 114 | SF4, B12 |
| 2 | 898 | 0.84 | 0.86 | 95 | SF4, B12 |
| 3 | 610 | 0.74 | 0.81 | 41 | EDO |
| 4 | 188 | 0.55 | 0.79 | 35 | empty |
| 5 | 171 | 0.47 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 605 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6WTE · Structure of radical S-adenosylmethionine methyltransferase, TsrM, from Kitasatospora… · 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 E4N8S5
- Elsewhere: RCSB PDB 6WTE · PDBe 6WTE · UniProt E4N8S5
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