Research workbench
X-ray structure of mycobacterium tuberculosis dodecin
Analyse X-ray structure of 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
- 2YIZ
- Type
- protein
- Length
- 272 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dodecin
- UniProt
- Q8VK10
- Ligands
- COA, FMN, CL
- Pockets
- 3 · best druggability 0.46
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dodecin | protein | 68 | 22% helix, 56% strand | Q8VK10 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains A, B, C, D
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, C, D, B
- CL · Chloride ion · ion · 2 copies · chains B, A, C
- GOL · Glycerol · additive · 5 copies · chains A, C, B, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.46 | 0.76 | 21 | FMN |
| 2 | 97 | 0.45 | 0.79 | 12 | GOL |
| 3 | 51 | 0.32 | 0.77 | 16 | COA |
Interfaces
5 interfaces between chains.
- A–D · 558 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 558 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 557 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 539 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 43 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2YIZ · X-ray structure of Mycobacterium tuberculosis Dodecin · 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 Q8VK10
- Elsewhere: RCSB PDB 2YIZ · PDBe 2YIZ · UniProt Q8VK10
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