Research workbench
X-ray structure of chemically engineered mycobacterium tuberculosis dodecin
Analyse X-ray structure of chemically engineered mycobacterium tuberculosis dodecin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YJ0
- Type
- protein
- Length
- 407 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dodecin
- UniProt
- Q8VK10
- Ligands
- 420, COA, FMN, CL, SO4
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F | Dodecin | protein | 68 | 19% helix, 56% strand | Q8VK10 |
| B | Dodecin | protein | 67 | 22% helix, 57% strand | Q8VK10 |
Ligands and binding sites
- 420 · N-[2-({[5-(dimethylamino)naphthalen-1-yl]sulfonyl}amino)ethyl]-2-iodoacetamide · ligand · 6 copies · chains A, B, C, E, D, F
- COA · Coenzyme A · ligand · 6 copies · chains A, B, C, E, D, F
- FMN · Flavin mononucleotide · ligand · 6 copies · chains A, B, D, E, C, F
- CL · Chloride ion · ion · 3 copies · chains B, C, E
- SO4 · Sulfate ion · ion · 2 copies · chains D, F, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 523 | 0.71 | 0.80 | 36 | FMN, 420 |
| 2 | 173 | 0.45 | 0.75 | 26 | 420, CL, FMN |
| 3 | 121 | 0.43 | 0.76 | 22 | empty |
| 4 | 86 | 0.43 | 0.79 | 14 | empty |
| 5 | 79 | 0.35 | 0.75 | 16 | empty |
Interfaces
9 interfaces between chains.
- A–B · 579 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 579 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 575 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 565 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 561 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 2YJ0 · X-ray structure of chemically engineered Mycobacterium tuberculosis Dodecin · the same entry in another collection · chain E against E, 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 Q8VK10
- Elsewhere: RCSB PDB 2YJ0 · PDBe 2YJ0 · UniProt Q8VK10
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