MolNFT v1 · #20815 · protein
Crystal structure and mechanism of a bacterial fluorinating enzyme, product complex
1RQR · 5'-fluoro-5'-deoxyadenosine synthase: “Crystal structure and mechanism of a bacterial fluorinating enzyme, product complex”. X-ray diffraction, 2 ligands (5FD, MET), 10 pockets (best druggability 0.80). MolNFT v1 #20815 on…
- PDB
- 1RQR
- 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
- 5FD, MET
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 5'-fluoro-5'-deoxyadenosine synthase (EC 2.5.1.63) | protein | 291 | 22% helix, 29% strand | Q70GK9 |
Ligands and binding sites
- 5FD · 5'-fluoro-5'-deoxyadenosine · ligand · 3 copies · chains A, B, C
- MET · Methionine · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.80 | 0.97 | 27 | 5FD, MET |
| 2 | 124 | 0.79 | 0.97 | 27 | 5FD, MET |
| 3 | 121 | 0.78 | 0.96 | 29 | 5FD, MET |
| 4 | 633 | 0.77 | 0.83 | 81 | empty |
| 5 | 316 | 0.67 | 0.82 | 46 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1638 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1612 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1605 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 1RQR · Crystal structure and mechanism of a bacterial fluorinating enzyme, product complex · 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 1RQR · PDBe 1RQR · UniProt Q70GK9
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