Research workbench
Crystal structure of the T. thermophilus dodecin R45A mutant
Analyse Crystal structure of the T. thermophilus dodecin R45A mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V19
- Type
- protein
- Length
- 810 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dodecin
- UniProt
- Q5SIE3
- Ligands
- COA, FMN, CL
- Pockets
- 15 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F, H, J | Dodecin | protein | 67 | 22% helix, 58% strand | Q5SIE3 |
| B, C, G, I, K, L | Dodecin | protein | 68 | 19% helix, 57% strand | Q5SIE3 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 12 copies · chains A, E, I, B, F, J, C, G, K, D, H, L
- FMN · Flavin mononucleotide · ligand · 10 copies · chains A, C, I, F, K, D, E, L, B, G, J, H
- CL · Chloride ion · ion · 5 copies · chains A, E, I, B, F, J, C, G, K, D, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 576 | 0.69 | 0.78 | 44 | FMN |
| 2 | 546 | 0.69 | 0.78 | 47 | FMN |
| 3 | 513 | 0.67 | 0.78 | 45 | FMN |
| 4 | 470 | 0.67 | 0.79 | 38 | FMN |
| 5 | 478 | 0.66 | 0.78 | 37 | empty |
Interfaces
24 interfaces between chains.
- C–K · 599 Ų buried · 12 hydrogen bonds · protein-protein
- B–J · 590 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 584 Ų buried · 9 hydrogen bonds · protein-protein
- C–G · 583 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 579 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2V19 · Crystal structure of the T. thermophilus dodecin R45A mutant · 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 2V19 · PDBe 2V19 · UniProt Q5SIE3
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