MolNFT v1 · #32948 · protein
X-ray crystal structure of 5'-fluorodeoxyadenosine synthase from streptomyces cattleya complexed with 2'DEOXY-adenosine
2C5H · 5'-fluoro-5'-deoxyadenosine synthase: “X-ray crystal structure of 5'-fluorodeoxyadenosine synthase from streptomyces cattleya complexed with…”. X-ray diffraction, 3 ligands (3D1, MET, CL), 9 pockets (best druggability 0.80). MolNFT…
- PDB
- 2C5H
- 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
- 3D1, MET, CL
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 20% 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 | 20% helix, 29% strand | Q70GK9 |
Ligands and binding sites
- 3D1 · (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol · ligand · 3 copies · chains A, B, C
- MET · Methionine · ligand · 2 copies · chains A, C, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.80 | 0.98 | 28 | MET, 3D1 |
| 2 | 119 | 0.79 | 0.98 | 27 | 3D1, MET |
| 3 | 108 | 0.78 | 0.98 | 28 | 3D1 |
| 4 | 308 | 0.78 | 0.89 | 35 | empty |
| 5 | 220 | 0.70 | 0.86 | 35 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1652 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1617 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1602 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 2C5H · X-ray crystal structure of 5'-fluorodeoxyadenosine synthase from Streptomyces cattleya… · the same entry in another collection · chain C against C, 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 2C5H · PDBe 2C5H · UniProt Q70GK9
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