Research workbench
Crystal structure of the T. thermophilus dodecin
Analyse Crystal structure of the T. thermophilus dodecin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V18
- Type
- protein
- Length
- 804 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dodecin
- UniProt
- Q5SIE3
- Ligands
- FMN, COA
- Pockets
- 18 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Dodecin | protein | 67 | 22% helix, 58% strand | Q5SIE3 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 12 copies · chains A, B, H, C, F, J, D, E, K, G, I, L
- COA · Coenzyme A · ligand · 9 copies · chains B, F, G, C, E, J, D, I, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 329 | 0.64 | 0.80 | 30 | FMN |
| 2 | 323 | 0.64 | 0.80 | 30 | FMN |
| 3 | 332 | 0.63 | 0.79 | 30 | FMN |
| 4 | 333 | 0.63 | 0.79 | 30 | FMN |
| 5 | 321 | 0.63 | 0.79 | 30 | FMN |
Interfaces
30 interfaces between chains.
- B–C · 637 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 635 Ų buried · 9 hydrogen bonds · protein-protein
- J–K · 635 Ų buried · 10 hydrogen bonds · protein-protein
- K–L · 629 Ų buried · 9 hydrogen bonds · protein-protein
- H–I · 626 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2V18 · Crystal structure of the T. thermophilus dodecin · the same entry in another collection · chain L against L, 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 Q5SIE3
- Elsewhere: RCSB PDB 2V18 · PDBe 2V18 · UniProt Q5SIE3
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