MolNFT v1 · #21226 · protein
Purine 2'-deoxyribosyltransferase + selenoinosine
1S3F · Purine trans deoxyribosylase: “Purine 2'-deoxyribosyltransferase + selenoinosine”. X-ray diffraction, 1 ligand (SNI), 9 pockets (best druggability 0.78). MolNFT v1 #21226 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1S3F
- Type
- protein
- Length
- 499 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine trans deoxyribosylase
- EC
- 2.4.2.6
- UniProt
- Q8RLY5
- Ligands
- SNI
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine trans deoxyribosylase (EC 2.4.2.6) | protein | 165 | 33% helix, 19% strand | Q8RLY5 |
| B, C | Purine trans deoxyribosylase (EC 2.4.2.6) | protein | 167 | 35% helix, 19% strand | Q8RLY5 |
Ligands and binding sites
- SNI · 9-(3,4-dihydroxy-5-hydroxymethyl-tetrahydro-furan-2-yl)-1,9-dihydro-purine-6-thione · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.78 | 0.90 | 38 | empty |
| 2 | 282 | 0.54 | 0.75 | 47 | SNI |
| 3 | 208 | 0.52 | 0.77 | 36 | SNI |
| 4 | 225 | 0.51 | 0.76 | 29 | SNI |
| 5 | 101 | 0.44 | 0.78 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 966 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 915 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 860 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1S3F · Purine 2'-deoxyribosyltransferase + selenoinosine · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8RLY5
- Elsewhere: RCSB PDB 1S3F · PDBe 1S3F · UniProt Q8RLY5
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