MolNFT v1 · #168858 · protein
Structure of radical S-adenosylmethionine methyltransferase, tsrm, from kitasatospora setae with tryptophan substrate and SAM analog (aza-SAM) bound
6WTF · Tryptophan-C2-methyltransferase containing B12-binding…: “Structure of radical S-adenosylmethionine methyltransferase, tsrm, from kitasatospora setae with tryptophan…”. X-ray diffraction, 4 ligands (SF4, B12, SA8), 9 pockets (best…
- PDB
- 6WTF
- Type
- protein
- Length
- 1,081 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan-C2-methyltransferase containing B12-binding domain
- UniProt
- E4N8S5
- Ligands
- SF4, B12, SA8, TRP
- Pockets
- 9 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan-C2-methyltransferase containing B12-binding domain | protein | 542 | 38% helix, 16% strand | E4N8S5 |
| B | Tryptophan-C2-methyltransferase containing B12-binding domain | protein | 539 | 38% helix, 17% strand | E4N8S5 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- B12 · Cobalamin · ligand · 2 copies · chains A, B
- SA8 · S-5'-azamethionine-5'-deoxyadenosine · ligand · 2 copies · chains A, B
- TRP · Tryptophan · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.88 | 0.90 | 92 | SF4, B12, SA8, TRP |
| 2 | 1163 | 0.88 | 0.89 | 95 | SF4, B12, SA8, TRP |
| 3 | 592 | 0.75 | 0.82 | 44 | empty |
| 4 | 147 | 0.38 | 0.72 | 24 | empty |
| 5 | 100 | 0.38 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 607 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6WTF · 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 6WTF · PDBe 6WTF · UniProt E4N8S5
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