Research workbench
Crystal structure and mechanism of a bacterial fluorinating enzyme
Analyse Crystal structure and mechanism of a bacterial fluorinating enzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RQP
- Type
- protein
- Length
- 873 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-fluoro-5'-deoxyadenosine synthase
- EC
- 2.5.1.63
- UniProt
- Q70GK9
- Ligands
- SAM
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 5'-fluoro-5'-deoxyadenosine synthase (EC 2.5.1.63) | protein | 291 | 21% helix, 30% strand | Q70GK9 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.79 | 0.98 | 26 | SAM |
| 2 | 116 | 0.78 | 0.97 | 29 | SAM |
| 3 | 108 | 0.78 | 0.98 | 28 | SAM |
| 4 | 314 | 0.77 | 0.89 | 34 | empty |
| 5 | 394 | 0.70 | 0.82 | 57 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1638 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1616 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1604 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1RQP · Crystal structure and mechanism of a bacterial fluorinating enzyme · the same entry in another collection · chain A against A, TM-score 1.00
- Q70GK9 · AlphaFold monomer V2.0 prediction for 5'-fluoro-5'-deoxy-adenosine synthase (Q70GK9) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q70GK9
- Elsewhere: RCSB PDB 1RQP · PDBe 1RQP · UniProt Q70GK9
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