Research workbench
Crystal structure of streptomyces tokunonesis tokk with hydroxycobalamin, 5'-deoxyadenosine, and methionine
Analyse Crystal structure of streptomyces tokunonesis tokk with hydroxycobalamin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KDX
- Type
- protein
- Length
- 1,322 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyltransferase tokk
- UniProt
- A0A6B9HEI0
- Ligands
- SF4, 5AD, B12, MET, K, CL
- Pockets
- 10 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyltransferase tokk | protein | 658 | 42% helix, 17% strand | A0A6B9HEI0 |
| B | Methyltransferase tokk | protein | 664 | 42% helix, 16% strand | A0A6B9HEI0 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- 5AD · 5'-deoxyadenosine · ligand · 2 copies · chains A, B
- B12 · Cobalamin · ligand · 2 copies · chains A, B
- MET · Methionine · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains B
- EDO · 1,2-ethanediol · additive · 21 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1048 | 0.88 | 0.89 | 118 | B12, SF4, 5AD, MET, EDO |
| 2 | 1157 | 0.87 | 0.88 | 138 | SF4, 5AD, B12, MET, EDO |
| 3 | 799 | 0.84 | 0.86 | 98 | K, EDO |
| 4 | 521 | 0.70 | 0.80 | 51 | empty |
| 5 | 379 | 0.69 | 0.82 | 44 | EDO |
Interfaces
1 interface between chains.
- A–B · 879 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7KDX · Crystal structure of Streptomyces toku sis TokK with hydroxycobalamin, 5'-deoxyadenosine… · 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 A0A6B9HEI0
- Elsewhere: RCSB PDB 7KDX · PDBe 7KDX · UniProt A0A6B9HEI0
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