MolNFT v1 · #32925 · protein
Crystal structure of the apo form of the 5'-fluoro-5'-deoxyadenosine synthase enzyme from streptomyces cattleya
2C4U: “Crystal structure of the apo form of the 5'-fluoro-5'-deoxyadenosine synthase enzyme from streptomyces…”. X-ray diffraction, 17 pockets (best druggability 0.81). MolNFT v1 #32925 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2C4U
- Type
- protein
- Length
- 1,746 residues
- Chains
- 6
- 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
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | 5'-fluoro-5'-deoxyadenosine synthase (EC 2.5.1.63) | protein | 291 | 21% helix, 30% strand | Q70GK9 |
Ligands and binding sites
- GOL · Glycerol · additive · 11 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 653 | 0.81 | 0.86 | 70 | GOL |
| 2 | 663 | 0.80 | 0.85 | 66 | GOL |
| 3 | 122 | 0.80 | 0.98 | 28 | GOL |
| 4 | 460 | 0.79 | 0.87 | 62 | GOL |
| 5 | 124 | 0.79 | 0.97 | 27 | empty |
Interfaces
9 interfaces between chains.
- D–F · 1601 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1600 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1600 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1597 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1575 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2C4U · Crystal structure of the apo form of the 5'-Fluoro-5'-deoxyadenosine synthase enzyme from… · the same entry in another collection · chain F against F, 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 2C4U · PDBe 2C4U · UniProt Q70GK9
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