MolNFT v2 · #51097 · protein
Crystal structure of the T. thermophilus dodecin R65A mutant
2UX9: “Crystal structure of the T. thermophilus dodecin R65A mutant”. X-ray diffraction at 1.4, 4 ligands (FMN, COA, NA), 4 pockets (best druggability 0.61). MolNFT v2 #51097 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2UX9
- Type
- protein
- Length
- 404 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.4
- Source
- THERMUS THERMOPHILUS
- Molecule
- Dodecin
- UniProt
- Q5SIE3
- Ligands
- FMN, COA, NA, PO4
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · resolution 1.4 · 3 distinct chains · 22% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dodecin | protein | 66 | 23% helix, 58% strand | Q5SIE3 |
| B, E | Dodecin | protein | 67 | 22% helix, 57% strand | Q5SIE3 |
| C, D, F | Dodecin | protein | 68 | 22% helix, 56% strand | Q5SIE3 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 6 copies · chains A, C, B, D, F, E
- COA · Coenzyme A · ligand · 6 copies · chains A, E, B, F, C, D
- NA · Sodium ion · metal · 4 copies · chains A, C, F
- PO4 · Phosphate ion · ion · 3 copies · chains B, F, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.61 | 0.79 | 30 | FMN |
| 2 | 123 | 0.41 | 0.76 | 23 | empty |
| 3 | 94 | 0.40 | 0.77 | 12 | empty |
| 4 | 53 | 0.31 | 0.76 | 12 | empty |
Interfaces
9 interfaces between chains.
- D–E · 620 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 612 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 610 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 609 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 609 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
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 2UX9 · PDBe 2UX9 · UniProt Q5SIE3
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