Research workbench
Structure of dodecin from streptomyces coelicolor
Analyse Structure of dodecin from streptomyces coelicolor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R1E
- Type
- protein
- Length
- 280 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dodecin
- UniProt
- Q9RCZ5
- Ligands
- FOR, FMN, COA, NA, SO4, CL
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dodecin | protein | 70 | 21% helix, 54% strand | Q9RCZ5 |
Ligands and binding sites
- FOR · Formyl group · ligand · 4 copies · chains A, C, B, D
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, C, D, B
- COA · Coenzyme A · ligand · 4 copies · chains A, C, B, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, C, B, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.56 | 0.82 | 26 | SO4 |
| 2 | 151 | 0.47 | 0.77 | 23 | FMN |
| 3 | 57 | 0.35 | 0.78 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–C · 637 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 584 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 566 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 563 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 61 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6R1E · Structure of dodecin from Streptomyces coelicolor · 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 Q9RCZ5
- Elsewhere: RCSB PDB 6R1E · PDBe 6R1E · UniProt Q9RCZ5
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